Association of parameter, software, and hardware variation with large-scale behavior across 57,000 climate models

PubMed Central

Knight, Christopher G.; Knight, Sylvia H. E.; Massey, Neil; Aina, Tolu; Christensen, Carl; Frame, Dave J.; Kettleborough, Jamie A.; Martin, Andrew; Pascoe, Stephen; Sanderson, Ben; Stainforth, David A.; Allen, Myles R.

2007-01-01

In complex spatial models, as used to predict the climate response to greenhouse gas emissions, parameter variation within plausible bounds has major effects on model behavior of interest. Here, we present an unprecedentedly large ensemble of >57,000 climate model runs in which 10 parameters, initial conditions, hardware, and software used to run the model all have been varied. We relate information about the model runs to large-scale model behavior (equilibrium sensitivity of global mean temperature to a doubling of carbon dioxide). We demonstrate that effects of parameter, hardware, and software variation are detectable, complex, and interacting. However, we find most of the effects of parameter variation are caused by a small subset of parameters. Notably, the entrainment coefficient in clouds is associated with 30% of the variation seen in climate sensitivity, although both low and high values can give high climate sensitivity. We demonstrate that the effect of hardware and software is small relative to the effect of parameter variation and, over the wide range of systems tested, may be treated as equivalent to that caused by changes in initial conditions. We discuss the significance of these results in relation to the design and interpretation of climate modeling experiments and large-scale modeling more generally. PMID:17640921

Instrument control software requirement specification for Extremely Large Telescopes

NASA Astrophysics Data System (ADS)

Young, Peter J.; Kiekebusch, Mario J.; Chiozzi, Gianluca

2010-07-01

Engineers in several observatories are now designing the next generation of optical telescopes, the Extremely Large Telescopes (ELT). These are very complex machines that will host sophisticated astronomical instruments to be used for a wide range of scientific studies. In order to carry out scientific observations, a software infrastructure is required to orchestrate the control of the multiple subsystems and functions. This paper will focus on describing the considerations, strategies and main issues related to the definition and analysis of the software requirements for the ELT's Instrument Control System using modern development processes and modelling tools like SysML.

Large-scale visualization projects for teaching software engineering.

PubMed

Müller, Christoph; Reina, Guido; Burch, Michael; Weiskopf, Daniel

2012-01-01

The University of Stuttgart's software engineering major complements the traditional computer science major with more practice-oriented education. Two-semester software projects in various application areas offered by the university's different computer science institutes are a successful building block in the curriculum. With this realistic, complex project setting, students experience the practice of software engineering, including software development processes, technologies, and soft skills. In particular, visualization-based projects are popular with students. Such projects offer them the opportunity to gain profound knowledge that would hardly be possible with only regular lectures and homework assignments.

You Can't Get There From Here! Problems and Potential Solutions in Developing New Classes of Complex Systems

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Rash, James L.; Truszkowski, Walter F.; Rouff, Christopher A.; Sterritt, Roy

2005-01-01

The explosion of capabilities and new products within the sphere of Information Technology (IT) has fostered widespread, overly optimistic opinions regarding the industry, based on common but unjustified assumptions of quality and correctness of software. These assumptions are encouraged by software producers and vendors, who at this late date have not succeeded in finding a way to overcome the lack of an automated, mathematically sound way to develop correct systems from requirements. NASA faces this dilemma as it envisages advanced mission concepts that involve large swarms of small spacecraft that will engage cooperatively to acheve science goals. Such missions entail levels of complexity that beg for new methods for system development far beyond today's methods, which are inadequate for ensuring correct behavior of large numbers of interacting intelligent mission elements. New system development techniques recently devised through NASA-led research will offer some innovative approaches to achieving correctness in complex system development, including autonomous swarm missions that exhibit emergent behavior, as well as general software products created by the computing industry.

Proposal for constructing an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Sims, Michael H.; Podolak, Esther; Mckay, Christopher P.; Thompson, David E.

1990-01-01

Scientific model building can be a time intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We believe that advanced software techniques can facilitate both the model building and model sharing process. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing and using models. The proposed tool will include an interactive intelligent graphical interface and a high level, domain specific, modeling language. As a testbed for this research, we propose development of a software prototype in the domain of planetary atmospheric modeling.

Simplified Deployment of Health Informatics Applications by Providing Docker Images.

PubMed

Löbe, Matthias; Ganslandt, Thomas; Lotzmann, Lydia; Mate, Sebastian; Christoph, Jan; Baum, Benjamin; Sariyar, Murat; Wu, Jie; Stäubert, Sebastian

2016-01-01

Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.

Application of Data Provenance in Healthcare Analytics Software: Information Visualisation of User Activities

PubMed Central

Xu, Shen; Rogers, Toby; Fairweather, Elliot; Glenn, Anthony; Curran, James; Curcin, Vasa

2018-01-01

Data provenance is a technique that describes the history of digital objects. In health data settings, it can be used to deliver auditability and transparency, and to achieve trust in a software system. However, implementing data provenance in analytics software at an enterprise level presents a different set of challenges from the research environments where data provenance was originally devised. In this paper, the challenges of reporting provenance information to the user is presented. Provenance captured from analytics software can be large and complex and visualizing a series of tasks over a long period can be overwhelming even for a domain expert, requiring visual aggregation mechanisms that fit with complex human cognitive activities involved in the process. This research studied how provenance-based reporting can be integrated into a health data analytics software, using the example of Atmolytics visual reporting tool. PMID:29888084

Architecture independent environment for developing engineering software on MIMD computers

NASA Technical Reports Server (NTRS)

Valimohamed, Karim A.; Lopez, L. A.

1990-01-01

Engineers are constantly faced with solving problems of increasing complexity and detail. Multiple Instruction stream Multiple Data stream (MIMD) computers have been developed to overcome the performance limitations of serial computers. The hardware architectures of MIMD computers vary considerably and are much more sophisticated than serial computers. Developing large scale software for a variety of MIMD computers is difficult and expensive. There is a need to provide tools that facilitate programming these machines. First, the issues that must be considered to develop those tools are examined. The two main areas of concern were architecture independence and data management. Architecture independent software facilitates software portability and improves the longevity and utility of the software product. It provides some form of insurance for the investment of time and effort that goes into developing the software. The management of data is a crucial aspect of solving large engineering problems. It must be considered in light of the new hardware organizations that are available. Second, the functional design and implementation of a software environment that facilitates developing architecture independent software for large engineering applications are described. The topics of discussion include: a description of the model that supports the development of architecture independent software; identifying and exploiting concurrency within the application program; data coherence; engineering data base and memory management.

Pragmatic quality metrics for evolutionary software development models

NASA Technical Reports Server (NTRS)

Royce, Walker

1990-01-01

Due to the large number of product, project, and people parameters which impact large custom software development efforts, measurement of software product quality is a complex undertaking. Furthermore, the absolute perspective from which quality is measured (customer satisfaction) is intangible. While we probably can't say what the absolute quality of a software product is, we can determine the relative quality, the adequacy of this quality with respect to pragmatic considerations, and identify good and bad trends during development. While no two software engineers will ever agree on an optimum definition of software quality, they will agree that the most important perspective of software quality is its ease of change. We can call this flexibility, adaptability, or some other vague term, but the critical characteristic of software is that it is soft. The easier the product is to modify, the easier it is to achieve any other software quality perspective. This paper presents objective quality metrics derived from consistent lifecycle perspectives of rework which, when used in concert with an evolutionary development approach, can provide useful insight to produce better quality per unit cost/schedule or to achieve adequate quality more efficiently. The usefulness of these metrics is evaluated by applying them to a large, real world, Ada project.

A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

DOE PAGES

Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

2008-01-01

Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

Software complex for geophysical data visualization

NASA Astrophysics Data System (ADS)

Kryukov, Ilya A.; Tyugin, Dmitry Y.; Kurkin, Andrey A.; Kurkina, Oxana E.

2013-04-01

The effectiveness of current research in geophysics is largely determined by the degree of implementation of the procedure of data processing and visualization with the use of modern information technology. Realistic and informative visualization of the results of three-dimensional modeling of geophysical processes contributes significantly into the naturalness of physical modeling and detailed view of the phenomena. The main difficulty in this case is to interpret the results of the calculations: it is necessary to be able to observe the various parameters of the three-dimensional models, build sections on different planes to evaluate certain characteristics and make a rapid assessment. Programs for interpretation and visualization of simulations are spread all over the world, for example, software systems such as ParaView, Golden Software Surfer, Voxler, Flow Vision and others. However, it is not always possible to solve the problem of visualization with the help of a single software package. Preprocessing, data transfer between the packages and setting up a uniform visualization style can turn into a long and routine work. In addition to this, sometimes special display modes for specific data are required and existing products tend to have more common features and are not always fully applicable to certain special cases. Rendering of dynamic data may require scripting languages that does not relieve the user from writing code. Therefore, the task was to develop a new and original software complex for the visualization of simulation results. Let us briefly list of the primary features that are developed. Software complex is a graphical application with a convenient and simple user interface that displays the results of the simulation. Complex is also able to interactively manage the image, resize the image without loss of quality, apply a two-dimensional and three-dimensional regular grid, set the coordinate axes with data labels and perform slice of data. The feature of geophysical data is their size. Detailed maps used in the simulations are large, thus rendering in real time can be difficult task even for powerful modern computers. Therefore, the performance of the software complex is an important aspect of this work. Complex is based on the latest version of graphic API: Microsoft - DirectX 11, which reduces overhead and harness the power of modern hardware. Each geophysical calculation is the adjustment of the mathematical model for a particular case, so the architecture of the complex visualization is created with the scalability and the ability to customize visualization objects, for better visibility and comfort. In the present study, software complex 'GeoVisual' was developed. One of the main features of this research is the use of bleeding-edge techniques of computer graphics in scientific visualization. The research was supported by The Ministry of education and science of Russian Federation, project 14.B37.21.0642.

MIS - The Human Connection

PubMed Central

Bush, Ian E.

1980-01-01

The lessons of the 70's with MIS were largely painful, often the same as those of the 60's, and were found in different phases on two continents. On examination this turns out to be true for many non-medical fields, true for systems programming, and thus a very general phenomenon. It is related to the functional complexity rather than to the sheer size of the software required, and above all to the relative neglect of human factors at all levels of software and hardware design. Simple hierarchical theory is a useful tool for analyzing complex systems and restoring the necessary dominance of common sense human factors. An example shows the very large effects of neglecting these factors on costs and benefits of MIS and their sub-systems.

High-energy physics software parallelization using database techniques

NASA Astrophysics Data System (ADS)

Argante, E.; van der Stok, P. D. V.; Willers, I.

1997-02-01

A programming model for software parallelization, called CoCa, is introduced that copes with problems caused by typical features of high-energy physics software. By basing CoCa on the database transaction paradimg, the complexity induced by the parallelization is for a large part transparent to the programmer, resulting in a higher level of abstraction than the native message passing software. CoCa is implemented on a Meiko CS-2 and on a SUN SPARCcenter 2000 parallel computer. On the CS-2, the performance is comparable with the performance of native PVM and MPI.

An Event-driven, Value-based, Pull Systems Engineering Scheduling Approach

DTIC Science & Technology

2012-03-01

engineering in rapid response environments has been difficult, particularly those where large, complex brownfield systems or systems of systems exist and...where large, complex brownfield systems or systems of systems exist and are constantly being updated with both short and long term software enhancements...2004. [13] B. Boehm, “Applying the Incremental Commitment Model to Brownfield System Development,” Proceedings, CSER, 2009. [14] A. Borshchev and A

A Comparison of Ada 83 and C++

DTIC Science & Technology

1991-06-01

developing large, complex, software systems with long lifetimes. Those interviewed for this study who are familiar with both Ada and C++ believe that Ada is...with those who are familiar with both languages, there was a clear preference for using Ada for large complex systems with long lifetimes. These...University, December 1990 Additions by Nelson H. Weiderman, June 1991. Chile Empresa Nacional de Aeronautica (ENAER), real-time avionics system, Data

Accelerating NASA GN&C Flight Software Development

NASA Technical Reports Server (NTRS)

Tamblyn, Scott; Henry, Joel; Rapp, John

2010-01-01

When the guidance, navigation, and control (GN&C) system for the Orion crew vehicle undergoes Critical Design Review (CDR), more than 90% of the flight software will already be developed - a first for NASA on a project of this scope and complexity. This achievement is due in large part to a new development approach using Model-Based Design.

NASA Applications for Computational Electromagnetic Analysis

NASA Technical Reports Server (NTRS)

Lewis, Catherine C.; Trout, Dawn H.; Krome, Mark E.; Perry, Thomas A.

2011-01-01

Computational Electromagnetic Software is used by NASA to analyze the compatibility of systems too large or too complex for testing. Recent advances in software packages and computer capabilities have made it possible to determine the effects of a transmitter inside a launch vehicle fairing, better analyze the environment threats, and perform on-orbit replacements with assured electromagnetic compatibility.

Software Reliability Issues Concerning Large and Safety Critical Software Systems

NASA Technical Reports Server (NTRS)

Kamel, Khaled; Brown, Barbara

1996-01-01

This research was undertaken to provide NASA with a survey of state-of-the-art techniques using in industrial and academia to provide safe, reliable, and maintainable software to drive large systems. Such systems must match the complexity and strict safety requirements of NASA's shuttle system. In particular, the Launch Processing System (LPS) is being considered for replacement. The LPS is responsible for monitoring and commanding the shuttle during test, repair, and launch phases. NASA built this system in the 1970's using mostly hardware techniques to provide for increased reliability, but it did so often using custom-built equipment, which has not been able to keep up with current technologies. This report surveys the major techniques used in industry and academia to ensure reliability in large and critical computer systems.

Pointo - a Low Cost Solution to Point Cloud Processing

NASA Astrophysics Data System (ADS)

Houshiar, H.; Winkler, S.

2017-11-01

With advance in technology access to data especially 3D point cloud data becomes more and more an everyday task. 3D point clouds are usually captured with very expensive tools such as 3D laser scanners or very time consuming methods such as photogrammetry. Most of the available softwares for 3D point cloud processing are designed for experts and specialists in this field and are usually very large software packages containing variety of methods and tools. This results in softwares that are usually very expensive to acquire and also very difficult to use. Difficulty of use is caused by complicated user interfaces that is required to accommodate a large list of features. The aim of these complex softwares is to provide a powerful tool for a specific group of specialist. However they are not necessary required by the majority of the up coming average users of point clouds. In addition to complexity and high costs of these softwares they generally rely on expensive and modern hardware and only compatible with one specific operating system. Many point cloud customers are not point cloud processing experts or willing to spend the high acquisition costs of these expensive softwares and hardwares. In this paper we introduce a solution for low cost point cloud processing. Our approach is designed to accommodate the needs of the average point cloud user. To reduce the cost and complexity of software our approach focuses on one functionality at a time in contrast with most available softwares and tools that aim to solve as many problems as possible at the same time. Our simple and user oriented design improve the user experience and empower us to optimize our methods for creation of an efficient software. In this paper we introduce Pointo family as a series of connected softwares to provide easy to use tools with simple design for different point cloud processing requirements. PointoVIEWER and PointoCAD are introduced as the first components of the Pointo family to provide a fast and efficient visualization with the ability to add annotation and documentation to the point clouds.

Design Optimization Toolkit: Users' Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aguilo Valentin, Miguel Alejandro

The Design Optimization Toolkit (DOTk) is a stand-alone C++ software package intended to solve complex design optimization problems. DOTk software package provides a range of solution methods that are suited for gradient/nongradient-based optimization, large scale constrained optimization, and topology optimization. DOTk was design to have a flexible user interface to allow easy access to DOTk solution methods from external engineering software packages. This inherent flexibility makes DOTk barely intrusive to other engineering software packages. As part of this inherent flexibility, DOTk software package provides an easy-to-use MATLAB interface that enables users to call DOTk solution methods directly from the MATLABmore » command window.« less

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1991-01-01

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

Control System Architectures, Technologies and Concepts for Near Term and Future Human Exploration of Space

NASA Technical Reports Server (NTRS)

Boulanger, Richard; Overland, David

2004-01-01

Technologies that facilitate the design and control of complex, hybrid, and resource-constrained systems are examined. This paper focuses on design methodologies, and system architectures, not on specific control methods that may be applied to life support subsystems. Honeywell and Boeing have estimated that 60-80Y0 of the effort in developing complex control systems is software development, and only 20-40% is control system development. It has also been shown that large software projects have failure rates of as high as 50-65%. Concepts discussed include the Unified Modeling Language (UML) and design patterns with the goal of creating a self-improving, self-documenting system design process. Successful architectures for control must not only facilitate hardware to software integration, but must also reconcile continuously changing software with much less frequently changing hardware. These architectures rely on software modules or components to facilitate change. Architecting such systems for change leverages the interfaces between these modules or components.

Drawing the PDB: Protein-Ligand Complexes in Two Dimensions.

PubMed

Stierand, Katrin; Rarey, Matthias

2010-12-09

The two-dimensional representation of molecules is a popular communication medium in chemistry and the associated scientific fields. Computational methods for drawing small molecules with and without manual investigation are well-established and widely spread in terms of numerous software tools. Concerning the planar depiction of molecular complexes, there is considerably less choice. We developed the software PoseView, which automatically generates two-dimensional diagrams of macromolecular complexes, showing the ligand, the interactions, and the interacting residues. All depicted molecules are drawn on an atomic level as structure diagrams; thus, the output plots are clearly structured and easily readable for the scientist. We tested the performance of PoseView in a large-scale application on nearly all druglike complexes of the PDB (approximately 200000 complexes); for more than 92% of the complexes considered for drawing, a layout could be computed. In the following, we will present the results of this application study.

Organizational Agility and Complex Enterprise System Innovations: A Mixed Methods Study of the Effects of Enterprise Systems on Organizational Agility

ERIC Educational Resources Information Center

Kharabe, Amol T.

2012-01-01

Over the last two decades, firms have operated in "increasingly" accelerated "high-velocity" dynamic markets, which require them to become "agile." During the same time frame, firms have increasingly deployed complex enterprise systems--large-scale packaged software "innovations" that integrate and automate…

The methodology of multi-viewpoint clustering analysis

NASA Technical Reports Server (NTRS)

Mehrotra, Mala; Wild, Chris

1993-01-01

One of the greatest challenges facing the software engineering community is the ability to produce large and complex computer systems, such as ground support systems for unmanned scientific missions, that are reliable and cost effective. In order to build and maintain these systems, it is important that the knowledge in the system be suitably abstracted, structured, and otherwise clustered in a manner which facilitates its understanding, manipulation, testing, and utilization. Development of complex mission-critical systems will require the ability to abstract overall concepts in the system at various levels of detail and to consider the system from different points of view. Multi-ViewPoint - Clustering Analysis MVP-CA methodology has been developed to provide multiple views of large, complicated systems. MVP-CA provides an ability to discover significant structures by providing an automated mechanism to structure both hierarchically (from detail to abstract) and orthogonally (from different perspectives). We propose to integrate MVP/CA into an overall software engineering life cycle to support the development and evolution of complex mission critical systems.

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

PubMed

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 for Leukocyte Biology.

Large Scale Screening of Low Cost Ferritic Steel Designs For Advanced Ultra Supercritical Boiler Using First Principles Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ouyang, Lizhi

Advanced Ultra Supercritical Boiler (AUSC) requires materials that can operate in corrosive environment at temperature and pressure as high as 760°C (or 1400°F) and 5000psi, respectively, while at the same time maintain good ductility at low temperature. We develop automated simulation software tools to enable fast large scale screening studies of candidate designs. While direct evaluation of creep rupture strength and ductility are currently not feasible, properties such as energy, elastic constants, surface energy, interface energy, and stack fault energy can be used to assess their relative ductility and creeping strength. We implemented software to automate the complex calculations tomore » minimize human inputs in the tedious screening studies which involve model structures generation, settings for first principles calculations, results analysis and reporting. The software developed in the project and library of computed mechanical properties of phases found in ferritic steels, many are complex solid solutions estimated for the first time, will certainly help the development of low cost ferritic steel for AUSC.« less

Autonomy Software: V&V Challenges and Characteristics

NASA Technical Reports Server (NTRS)

Schumann, Johann; Visser, Willem

2006-01-01

The successful operation of unmanned air vehicles requires software with a high degree of autonomy. Only if high level functions can be carried out without human control and intervention, complex missions in a changing and potentially unknown environment can be carried out successfully. Autonomy software is highly mission and safety critical: failures, caused by flaws in the software cannot only jeopardize the mission, but could also endanger human life (e.g., a crash of an UAV in a densely populated area). Due to its large size, high complexity, and use of specialized algorithms (planner, constraint-solver, etc.), autonomy software poses specific challenges for its verification, validation, and certification. -- - we have carried out a survey among researchers aid scientists at NASA to study these issues. In this paper, we will present major results of this study, discussing the broad spectrum. of notions and characteristics of autonomy software and its challenges for design and development. A main focus of this survey was to evaluate verification and validation (V&V) issues and challenges, compared to the development of "traditional" safety-critical software. We will discuss important issues in V&V of autonomous software and advanced V&V tools which can help to mitigate software risks. Results of this survey will help to identify and understand safety concerns in autonomy software and will lead to improved strategies for mitigation of these risks.

TMT approach to observatory software development process

NASA Astrophysics Data System (ADS)

Buur, Hanne; Subramaniam, Annapurni; Gillies, Kim; Dumas, Christophe; Bhatia, Ravinder

2016-07-01

The purpose of the Observatory Software System (OSW) is to integrate all software and hardware components of the Thirty Meter Telescope (TMT) to enable observations and data capture; thus it is a complex software system that is defined by four principal software subsystems: Common Software (CSW), Executive Software (ESW), Data Management System (DMS) and Science Operations Support System (SOSS), all of which have interdependencies with the observatory control systems and data acquisition systems. Therefore, the software development process and plan must consider dependencies to other subsystems, manage architecture, interfaces and design, manage software scope and complexity, and standardize and optimize use of resources and tools. Additionally, the TMT Observatory Software will largely be developed in India through TMT's workshare relationship with the India TMT Coordination Centre (ITCC) and use of Indian software industry vendors, which adds complexity and challenges to the software development process, communication and coordination of activities and priorities as well as measuring performance and managing quality and risk. The software project management challenge for the TMT OSW is thus a multi-faceted technical, managerial, communications and interpersonal relations challenge. The approach TMT is using to manage this multifaceted challenge is a combination of establishing an effective geographically distributed software team (Integrated Product Team) with strong project management and technical leadership provided by the TMT Project Office (PO) and the ITCC partner to manage plans, process, performance, risk and quality, and to facilitate effective communications; establishing an effective cross-functional software management team composed of stakeholders, OSW leadership and ITCC leadership to manage dependencies and software release plans, technical complexities and change to approved interfaces, architecture, design and tool set, and to facilitate effective communications; adopting an agile-based software development process across the observatory to enable frequent software releases to help mitigate subsystem interdependencies; defining concise scope and work packages for each of the OSW subsystems to facilitate effective outsourcing of software deliverables to the ITCC partner, and to enable performance monitoring and risk management. At this stage, the architecture and high-level design of the software system has been established and reviewed. During construction each subsystem will have a final design phase with reviews, followed by implementation and testing. The results of the TMT approach to the Observatory Software development process will only be preliminary at the time of the submittal of this paper, but it is anticipated that the early results will be a favorable indication of progress.

An implementation of the distributed programming structural synthesis system (PROSSS)

NASA Technical Reports Server (NTRS)

Rogers, J. L., Jr.

1981-01-01

A method is described for implementing a flexible software system that combines large, complex programs with small, user-supplied, problem-dependent programs and that distributes their execution between a mainframe and a minicomputer. The Programming Structural Synthesis System (PROSSS) was the specific software system considered. The results of such distributed implementation are flexibility of the optimization procedure organization and versatility of the formulation of constraints and design variables.

System Engineering Concept Demonstration, System Engineering Needs. Volume 2

DTIC Science & Technology

1992-12-01

changeability, and invisibility. "Software entities are perhaps more complex for their size than any other human construct..." In addition, software is... human actions and interactions that often fail or insufficient in large organizations. Specific needs in this area include the following: " Each...needed to accomplish incremental review and critique of information. * Automi ..-’ metrics support is needed for the measuring ikey quality aspects of

A finite element formulation for scattering from electrically large 2-dimensional structures

NASA Technical Reports Server (NTRS)

Ross, Daniel C.; Volakis, John L.

1992-01-01

A finite element formulation is given using the scattered field approach with a fictitious material absorber to truncate the mesh. The formulation includes the use of arbitrary approximation functions so that more accurate results can be achieved without any modification to the software. Additionally, non-polynomial approximation functions can be used, including complex approximation functions. The banded system that results is solved with an efficient sparse/banded iterative scheme and as a consequence, large structures can be analyzed. Results are given for simple cases to verify the formulation and also for large, complex geometries.

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

Digital Library Storage using iRODS Data Grids

NASA Astrophysics Data System (ADS)

Hedges, Mark; Blanke, Tobias; Hasan, Adil

Digital repository software provides a powerful and flexible infrastructure for managing and delivering complex digital resources and metadata. However, issues can arise in managing the very large, distributed data files that may constitute these resources. This paper describes an implementation approach that combines the Fedora digital repository software with a storage layer implemented as a data grid, using the iRODS middleware developed by DICE (Data Intensive Cyber Environments) as the successor to SRB. This approach allows us to use Fedoras flexible architecture to manage the structure of resources and to provide application- layer services to users. The grid-based storage layer provides efficient support for managing and processing the underlying distributed data objects, which may be very large (e.g. audio-visual material). The Rule Engine built into iRODS is used to integrate complex workflows at the data level that need not be visible to users, e.g. digital preservation functionality.

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

PubMed Central

Johnson, Z. P.; Eady, R. D.; Ahmad, S. F.; Agravat, S.; Morris, T; Else, J; Lank, S. M.; Wiseman, R. W.; O’Connor, D. H.; Penedo, M. C. T.; Larsen, C. P.

2012-01-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permitsmultiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox onWindows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie. kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo, user name: imsdemo7@gmail.com and password: imsdemo. PMID:22080300

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets.

PubMed

Johnson, Z P; Eady, R D; Ahmad, S F; Agravat, S; Morris, T; Else, J; Lank, S M; Wiseman, R W; O'Connor, D H; Penedo, M C T; Larsen, C P; Kean, L S

2012-04-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

Modeling a distributed environment for a petroleum reservoir engineering application with software product line

NASA Astrophysics Data System (ADS)

de Faria Scheidt, Rafael; Vilain, Patrícia; Dantas, M. A. R.

2014-10-01

Petroleum reservoir engineering is a complex and interesting field that requires large amount of computational facilities to achieve successful results. Usually, software environments for this field are developed without taking care out of possible interactions and extensibilities required by reservoir engineers. In this paper, we present a research work which it is characterized by the design and implementation based on a software product line model for a real distributed reservoir engineering environment. Experimental results indicate successfully the utilization of this approach for the design of distributed software architecture. In addition, all components from the proposal provided greater visibility of the organization and processes for the reservoir engineers.

The Many Faces of a Software Engineer in a Research Community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marinovici, Maria C.; Kirkham, Harold

2013-10-14

The ability to gather, analyze and make decisions based on real world data is changing nearly every field of human endeavor. These changes are particularly challenging for software engineers working in a scientific community, designing and developing large, complex systems. To avoid the creation of a communications gap (almost a language barrier), the software engineers should possess an ‘adaptive’ skill. In the science and engineering research community, the software engineers must be responsible for more than creating mechanisms for storing and analyzing data. They must also develop a fundamental scientific and engineering understanding of the data. This paper looks atmore » the many faces that a software engineer should have: developer, domain expert, business analyst, security expert, project manager, tester, user experience professional, etc. Observations made during work on a power-systems scientific software development are analyzed and extended to describe more generic software development projects.« less

Idea Paper: The Lifecycle of Software for Scientific Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubey, Anshu; McInnes, Lois C.

The software lifecycle is a well researched topic that has produced many models to meet the needs of different types of software projects. However, one class of projects, software development for scientific computing, has received relatively little attention from lifecycle researchers. In particular, software for end-to-end computations for obtaining scientific results has received few lifecycle proposals and no formalization of a development model. An examination of development approaches employed by the teams implementing large multicomponent codes reveals a great deal of similarity in their strategies. This idea paper formalizes these related approaches into a lifecycle model for end-to-end scientific applicationmore » software, featuring loose coupling between submodels for development of infrastructure and scientific capability. We also invite input from stakeholders to converge on a model that captures the complexity of this development processes and provides needed lifecycle guidance to the scientific software community.« less

Equilibrium expert: an add-in to Microsoft Excel for multiple binding equilibrium simulations and parameter estimations.

PubMed

Raguin, Olivier; Gruaz-Guyon, Anne; Barbet, Jacques

2002-11-01

An add-in to Microsoft Excel was developed to simulate multiple binding equilibriums. A partition function, readily written even when the equilibrium is complex, describes the experimental system. It involves the concentrations of the different free molecular species and of the different complexes present in the experiment. As a result, the software is not restricted to a series of predefined experimental setups but can handle a large variety of problems involving up to nine independent molecular species. Binding parameters are estimated by nonlinear least-square fitting of experimental measurements as supplied by the user. The fitting process allows user-defined weighting of the experimental data. The flexibility of the software and the way it may be used to describe common experimental situations and to deal with usual problems such as tracer reactivity or nonspecific binding is demonstrated by a few examples. The software is available free of charge upon request.

Strategies for responding to RAC requests electronically.

PubMed

Schramm, Michael

2012-04-01

Providers that would like to respond to complex RAC reviews electronically should consider three strategies: Invest in an EHR software package or a high-powered scanner that can quickly scan large amounts of paper. Implement an audit software platform that will allow providers to manage the entire audit process in one place. Use a CONNECT-compatible gateway capable of accessing the Nationwide Health Information Network (the network on which the electronic submission of medical documentation program runs).

Microprocessor based implementation of attitude and shape control of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1984-01-01

The feasibility of off the shelf eight bit and 16 bit microprocessors to implement linear state variable feedback control laws and assessing the real time response to spacecraft dynamics is studied. The complexity of the dynamic model is described along with the appropriate software. An experimental setup of a beam, microprocessor system for implementing the control laws and the needed generalized software to implement any state variable feedback control system is included.

Planetary Data Workshop, Part 2

NASA Technical Reports Server (NTRS)

1984-01-01

Technical aspects of the Planetary Data System (PDS) are addressed. Methods and tools for maintaining and accessing large, complex sets of data are discussed. The specific software and applications needed for processing imaging and non-imaging science data are reviewed. The need for specific software that provides users with information on the location and geometry of scientific observations is discussed. Computer networks and user interface to the PDS are covered along with Computer hardware available to this data system.

77 FR 50726 - Software Requirement Specifications for Digital Computer Software and Complex Electronics Used in...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... Computer Software and Complex Electronics Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear...-1209, ``Software Requirement Specifications for Digital Computer Software and Complex Electronics used... Electronics Engineers (ANSI/IEEE) Standard 830-1998, ``IEEE Recommended Practice for Software Requirements...

Shuttle avionics software trials, tribulations and success

NASA Technical Reports Server (NTRS)

Henderson, O. L.

1985-01-01

The early problems and the solutions developed to provide the required quality software needed to support the space shuttle engine development program are described. The decision to use a programmable digital control system on the space shuttle engine was primarily based upon the need for a flexible control system capable of supporting the total engine mission on a large complex pump fed engine. The mission definition included all control phases from ground checkout through post shutdown propellant dumping. The flexibility of the controller through reprogrammable software allowed the system to respond to the technical challenges and innovation required to develop both the engine and controller hardware. This same flexibility, however, placed a severe strain on the capability of the software development and verification organization. The overall development program required that the software facility accommodate significant growth in both the software requirements and the number of software packages delivered. This challenge was met by reorganization and evolution in the process of developing and verifying software.

SU-E-T-76: A Software System to Monitor VMAT Plan Complexity in a Large Radiotherapy Centre

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arumugam, S; Xing, A; Ingham Institute, Sydney, NSW

2015-06-15

Purpose: To develop a system that analyses and reports the complexity of Volumetric Modulated Arc Therapy (VMAT) plans to aid in the decision making for streamlining patient specific dosimetric quality assurance (QA) tests. Methods: A software system, Delcheck, was developed in-house to calculate VMAT plan and delivery complexity using the treatment delivery file. Delcheck has the functionality to calculate multiple plan complexity metrics including the Li-Xing Modulation Index (LI-MI), multiplicative combination of Leaf Travel and Modulation Complexity Score (LTMCSv), Monitor Units per prescribed dose (MU/D) and the delivery complexity index (MIt) that incorporates the modulation of dose rate, leaf speedmore » and gantry speed. Delcheck includes database functionality to store and compare plan metrics for a specified treatment site. The overall plan and delivery complexity is assessed based on the 95% conformance limit of the complexity metrics as Similar, More or Less complex. The functionality of the software was tested using 42 prostate conventional, 10 prostate SBRT and 15 prostate bed VMAT plans generated for an Elekta linear accelerator. Results: The mean(σ) of LI-MI for conventional, SBRT and prostate bed plans were 1690(486), 3215.4(1294) and 3258(982) respectively. The LTMCSv of the studied categories were 0.334(0.05), 0.325(0.07) and 0.3112(0.09). The MU/D of the studied categories were 2.4(0.4), 2.7(0.7) and 2.5(0.5). The MIt of the studied categories were 21.6(3.4), 18.2(3.0) and 35.9(6.6). The values of the complexity metrics show that LI-MI appeared to resolve the plan complexity better than LTMCSv and MU/D. The MIt value increased as the delivery complexity increased. Conclusion: The developed software was shown to be working as expected. In studied treatment categories Prostate bed plans are more complex in both plan and delivery and SBRT is more complex in plan and less complex in delivery as demonstrated by LI-MI and MIt. This project was funded through a Cancer Council NSW Project Grant (RG14-11)« less

Distributed Administration of Online Learning Accounts

ERIC Educational Resources Information Center

Gamrat, Betsy

2004-01-01

Distance learning is a vital part of today's educational environment. Using complex technology, schools are able to connect instructors and students across geographic, physical, and temporal boundaries. Sophisticated software and world-wide connectivity create virtual classrooms that span the globe. These large, accessible, asynchronous,…

Automated Software Development Workstation (ASDW)

NASA Technical Reports Server (NTRS)

Fridge, Ernie

1990-01-01

Software development is a serious bottleneck in the construction of complex automated systems. An increase of the reuse of software designs and components has been viewed as a way to relieve this bottleneck. One approach to achieving software reusability is through the development and use of software parts composition systems. A software parts composition system is a software development environment comprised of a parts description language for modeling parts and their interfaces, a catalog of existing parts, a composition editor that aids a user in the specification of a new application from existing parts, and a code generator that takes a specification and generates an implementation of a new application in a target language. The Automated Software Development Workstation (ASDW) is an expert system shell that provides the capabilities required to develop and manipulate these software parts composition systems. The ASDW is now in Beta testing at the Johnson Space Center. Future work centers on responding to user feedback for capability and usability enhancement, expanding the scope of the software lifecycle that is covered, and in providing solutions to handling very large libraries of reusable components.

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

PubMed Central

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

Observation Scheduling System

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Tran, Daniel Q.; Rabideau, Gregg R.; Schaffer, Steven R.

2011-01-01

Software has been designed to schedule remote sensing with the Earth Observing One spacecraft. The software attempts to satisfy as many observation requests as possible considering each against spacecraft operation constraints such as data volume, thermal, pointing maneuvers, and others. More complex constraints such as temperature are approximated to enable efficient reasoning while keeping the spacecraft within safe limits. Other constraints are checked using an external software library. For example, an attitude control library is used to determine the feasibility of maneuvering between pairs of observations. This innovation can deal with a wide range of spacecraft constraints and solve large scale scheduling problems like hundreds of observations and thousands of combinations of observation sequences.

Unmanned Vehicle Guidance Using Video Camera/Vehicle Model

NASA Technical Reports Server (NTRS)

Sutherland, T.

1999-01-01

A video guidance sensor (VGS) system has flown on both STS-87 and STS-95 to validate a single camera/target concept for vehicle navigation. The main part of the image algorithm was the subtraction of two consecutive images using software. For a nominal size image of 256 x 256 pixels this subtraction can take a large portion of the time between successive frames in standard rate video leaving very little time for other computations. The purpose of this project was to integrate the software subtraction into hardware to speed up the subtraction process and allow for more complex algorithms to be performed, both in hardware and software.

GRAMM-X public web server for protein–protein docking

PubMed Central

Tovchigrechko, Andrey; Vakser, Ilya A.

2006-01-01

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track. PMID:16845016

A Decision Tool that Combines Discrete Event Software Process Models with System Dynamics Pieces for Software Development Cost Estimation and Analysis

NASA Technical Reports Server (NTRS)

Mizell, Carolyn Barrett; Malone, Linda

2007-01-01

The development process for a large software development project is very complex and dependent on many variables that are dynamic and interrelated. Factors such as size, productivity and defect injection rates will have substantial impact on the project in terms of cost and schedule. These factors can be affected by the intricacies of the process itself as well as human behavior because the process is very labor intensive. The complex nature of the development process can be investigated with software development process models that utilize discrete event simulation to analyze the effects of process changes. The organizational environment and its effects on the workforce can be analyzed with system dynamics that utilizes continuous simulation. Each has unique strengths and the benefits of both types can be exploited by combining a system dynamics model and a discrete event process model. This paper will demonstrate how the two types of models can be combined to investigate the impacts of human resource interactions on productivity and ultimately on cost and schedule.

An expert system executive for automated assembly of large space truss structures

NASA Technical Reports Server (NTRS)

Allen, Cheryl L.

1993-01-01

Langley Research Center developed a unique test bed for investigating the practical problems associated with the assembly of large space truss structures using robotic manipulators. The test bed is the result of an interdisciplinary effort that encompasses the full spectrum of assembly problems - from the design of mechanisms to the development of software. The automated structures assembly test bed and its operation are described, the expert system executive and its development are detailed, and the planned system evolution is discussed. Emphasis is on the expert system implementation of the program executive. The executive program must direct and reliably perform complex assembly tasks with the flexibility to recover from realistic system errors. The employment of an expert system permits information that pertains to the operation of the system to be encapsulated concisely within a knowledge base. This consolidation substantially reduced code, increased flexibility, eased software upgrades, and realized a savings in software maintenance costs.

Complexity as a Factor of Quality and Cost in Large Scale Software Development.

DTIC Science & Technology

1979-12-01

allocating testing resources." [69 69I V. THE ROLE OF COMPLEXITY IN RESOURCE ESTIMATION AND ALLOCATION A. GENERAL It can be argued that blame for the...and allocation of testing resource by - identifying independent substructures and - identifying heavily used logic paths. 2. Setting a Design Threshold... RESOURCE ESTIMATION -------- 70 1. New Dynamic Field ------------------------- 70 2. Quality and Testing ----------------------- 71 3. Programming Units of

An evaluation of superminicomputers for thermal analysis

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Vidal, J. B.; Jones, G. K.

1982-01-01

The use of superminicomputers for solving a series of increasingly complex thermal analysis problems is investigated. The approach involved (1) installation and verification of the SPAR thermal analyzer software on superminicomputers at Langley Research Center and Goddard Space Flight Center, (2) solution of six increasingly complex thermal problems on this equipment, and (3) comparison of solution (accuracy, CPU time, turnaround time, and cost) with solutions on large mainframe computers.

A workflow learning model to improve geovisual analytics utility

PubMed Central

Roth, Robert E; MacEachren, Alan M; McCabe, Craig A

2011-01-01

Introduction This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. Objectives The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. Methodology The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. Results/Conclusions In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009. PMID:21983545

A workflow learning model to improve geovisual analytics utility.

PubMed

Roth, Robert E; Maceachren, Alan M; McCabe, Craig A

2009-01-01

INTRODUCTION: This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. OBJECTIVES: The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. METHODOLOGY: The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. RESULTS/CONCLUSIONS: In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009.

Learning Human Aspects of Collaborative Software Development

ERIC Educational Resources Information Center

Hadar, Irit; Sherman, Sofia; Hazzan, Orit

2008-01-01

Collaboration has become increasingly widespread in the software industry as systems have become larger and more complex, adding human complexity to the technological complexity already involved in developing software systems. To deal with this complexity, human-centric software development methods, such as Extreme Programming and other agile…

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

NASA Astrophysics Data System (ADS)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical models.

Leveraging Modeling Approaches: Reaction Networks and Rules

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high resolution and/or high throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatio-temporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks – the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks. PMID:22161349

Leveraging modeling approaches: reaction networks and rules.

PubMed

Blinov, Michael L; Moraru, Ion I

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.

Averting Denver Airports on a Chip

NASA Technical Reports Server (NTRS)

Sullivan, Kevin J.

1995-01-01

As a result of recent advances in software engineering capabilities, we are now in a more stable environment. De-facto hardware and software standards are emerging. Work on software architecture and design patterns signals a consensus on the importance of early system-level design decisions, and agreements on the uses of certain paradigmatic software structures. We now routinely build systems that would have been risky or infeasible a few years ago. Unfortunately, technological developments threaten to destabilize software design again. Systems designed around novel computing and peripheral devices will spark ambitious new projects that will stress current software design and engineering capabilities. Micro-electro-mechanical systems (MEMS) and related technologies provide the physical basis for new systems with the potential to produce this kind of destabilizing effect. One important response to anticipated software engineering and design difficulties is carefully directed engineering-scientific research. Two specific problems meriting substantial research attention are: A lack of sufficient means to build software systems by generating, extending, specializing, and integrating large-scale reusable components; and a lack of adequate computational and analytic tools to extend and aid engineers in maintaining intellectual control over complex software designs.

Minimus: a fast, lightweight genome assembler.

PubMed

Sommer, Daniel D; Delcher, Arthur L; Salzberg, Steven L; Pop, Mihai

2007-02-26

Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.

Conducting Automated Test Assembly Using the Premium Solver Platform Version 7.0 with Microsoft Excel and the Large-Scale LP/QP Solver Engine Add-In

ERIC Educational Resources Information Center

Cor, Ken; Alves, Cecilia; Gierl, Mark J.

2008-01-01

This review describes and evaluates a software add-in created by Frontline Systems, Inc., that can be used with Microsoft Excel 2007 to solve large, complex test assembly problems. The combination of Microsoft Excel 2007 with the Frontline Systems Premium Solver Platform is significant because Microsoft Excel is the most commonly used spreadsheet…

USSR and Eastern Europe Scientific Abstracts, Cybernetics, Computers, and Automation Technology, Number 26

DTIC Science & Technology

1977-01-26

Sisteme Matematicheskogo Obespecheniya YeS EVM [ Applied Programs in the Software System for the Unified System of Computers], by A. Ye. Fateyev, A. I...computerized systems are most effective in large production complexes , in which the level of utilization of computers can be as high as 500,000...performance of these tasks could be furthered by the complex introduction of electronic computers in automated control systems. The creation of ASU

Theoretical and software considerations for nonlinear dynamic analysis

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1983-01-01

In the finite element method for structural analysis, it is generally necessary to discretize the structural model into a very large number of elements to accurately evaluate displacements, strains, and stresses. As the complexity of the model increases, the number of degrees of freedom can easily exceed the capacity of present-day software system. Improvements of structural analysis software including more efficient use of existing hardware and improved structural modeling techniques are discussed. One modeling technique that is used successfully in static linear and nonlinear analysis is multilevel substructuring. This research extends the use of multilevel substructure modeling to include dynamic analysis and defines the requirements for a general purpose software system capable of efficient nonlinear dynamic analysis. The multilevel substructuring technique is presented, the analytical formulations and computational procedures for dynamic analysis and nonlinear mechanics are reviewed, and an approach to the design and implementation of a general purpose structural software system is presented.

A bridge role metric model for nodes in software networks.

PubMed

Li, Bo; Feng, Yanli; Ge, Shiyu; Li, Dashe

2014-01-01

A bridge role metric model is put forward in this paper. Compared with previous metric models, our solution of a large-scale object-oriented software system as a complex network is inherently more realistic. To acquire nodes and links in an undirected network, a new model that presents the crucial connectivity of a module or the hub instead of only centrality as in previous metric models is presented. Two previous metric models are described for comparison. In addition, it is obvious that the fitting curve between the Bre results and degrees can well be fitted by a power law. The model represents many realistic characteristics of actual software structures, and a hydropower simulation system is taken as an example. This paper makes additional contributions to an accurate understanding of module design of software systems and is expected to be beneficial to software engineering practices.

A Bridge Role Metric Model for Nodes in Software Networks

PubMed Central

Li, Bo; Feng, Yanli; Ge, Shiyu; Li, Dashe

2014-01-01

A bridge role metric model is put forward in this paper. Compared with previous metric models, our solution of a large-scale object-oriented software system as a complex network is inherently more realistic. To acquire nodes and links in an undirected network, a new model that presents the crucial connectivity of a module or the hub instead of only centrality as in previous metric models is presented. Two previous metric models are described for comparison. In addition, it is obvious that the fitting curve between the results and degrees can well be fitted by a power law. The model represents many realistic characteristics of actual software structures, and a hydropower simulation system is taken as an example. This paper makes additional contributions to an accurate understanding of module design of software systems and is expected to be beneficial to software engineering practices. PMID:25364938

Intelligent fault management for the Space Station active thermal control system

NASA Technical Reports Server (NTRS)

Hill, Tim; Faltisco, Robert M.

1992-01-01

The Thermal Advanced Automation Project (TAAP) approach and architecture is described for automating the Space Station Freedom (SSF) Active Thermal Control System (ATCS). The baseline functionally and advanced automation techniques for Fault Detection, Isolation, and Recovery (FDIR) will be compared and contrasted. Advanced automation techniques such as rule-based systems and model-based reasoning should be utilized to efficiently control, monitor, and diagnose this extremely complex physical system. TAAP is developing advanced FDIR software for use on the SSF thermal control system. The goal of TAAP is to join Knowledge-Based System (KBS) technology, using a combination of rules and model-based reasoning, with conventional monitoring and control software in order to maximize autonomy of the ATCS. TAAP's predecessor was NASA's Thermal Expert System (TEXSYS) project which was the first large real-time expert system to use both extensive rules and model-based reasoning to control and perform FDIR on a large, complex physical system. TEXSYS showed that a method is needed for safely and inexpensively testing all possible faults of the ATCS, particularly those potentially damaging to the hardware, in order to develop a fully capable FDIR system. TAAP therefore includes the development of a high-fidelity simulation of the thermal control system. The simulation provides realistic, dynamic ATCS behavior and fault insertion capability for software testing without hardware related risks or expense. In addition, thermal engineers will gain greater confidence in the KBS FDIR software than was possible prior to this kind of simulation testing. The TAAP KBS will initially be a ground-based extension of the baseline ATCS monitoring and control software and could be migrated on-board as additional computation resources are made available.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1993-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a testbed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1992-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a test bed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Challenges in Managing Trustworthy Large-scale Digital Science

NASA Astrophysics Data System (ADS)

Evans, B. J. K.

2017-12-01

The increased use of large-scale international digital science has opened a number of challenges for managing, handling, using and preserving scientific information. The large volumes of information are driven by three main categories - model outputs including coupled models and ensembles, data products that have been processing to a level of usability, and increasingly heuristically driven data analysis. These data products are increasingly the ones that are usable by the broad communities, and far in excess of the raw instruments data outputs. The data, software and workflows are then shared and replicated to allow broad use at an international scale, which places further demands of infrastructure to support how the information is managed reliably across distributed resources. Users necessarily rely on these underlying "black boxes" so that they are productive to produce new scientific outcomes. The software for these systems depend on computational infrastructure, software interconnected systems, and information capture systems. This ranges from the fundamentals of the reliability of the compute hardware, system software stacks and libraries, and the model software. Due to these complexities and capacity of the infrastructure, there is an increased emphasis of transparency of the approach and robustness of the methods over the full reproducibility. Furthermore, with large volume data management, it is increasingly difficult to store the historical versions of all model and derived data. Instead, the emphasis is on the ability to access the updated products and the reliability by which both previous outcomes are still relevant and can be updated for the new information. We will discuss these challenges and some of the approaches underway that are being used to address these issues.

Software automation tools for increased throughput metabolic soft-spot identification in early drug discovery.

PubMed

Zelesky, Veronica; Schneider, Richard; Janiszewski, John; Zamora, Ismael; Ferguson, James; Troutman, Matthew

2013-05-01

The ability to supplement high-throughput metabolic clearance data with structural information defining the site of metabolism should allow design teams to streamline their synthetic decisions. However, broad application of metabolite identification in early drug discovery has been limited, largely due to the time required for data review and structural assignment. The advent of mass defect filtering and its application toward metabolite scouting paved the way for the development of software automation tools capable of rapidly identifying drug-related material in complex biological matrices. Two semi-automated commercial software applications, MetabolitePilot™ and Mass-MetaSite™, were evaluated to assess the relative speed and accuracy of structural assignments using data generated on a high-resolution MS platform. Review of these applications has demonstrated their utility in providing accurate results in a time-efficient manner, leading to acceleration of metabolite identification initiatives while highlighting the continued need for biotransformation expertise in the interpretation of more complex metabolic reactions.

Real-Time Spatio-Temporal Twice Whitening for MIMO Energy Detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humble, Travis S; Mitra, Pramita; Barhen, Jacob

2010-01-01

While many techniques exist for local spectrum sensing of a primary user, each represents a computationally demanding task to secondary user receivers. In software-defined radio, computational complexity lengthens the time for a cognitive radio to recognize changes in the transmission environment. This complexity is even more significant for spatially multiplexed receivers, e.g., in SIMO and MIMO, where the spatio-temporal data sets grow in size with the number of antennae. Limits on power and space for the processor hardware further constrain SDR performance. In this report, we discuss improvements in spatio-temporal twice whitening (STTW) for real-time local spectrum sensing by demonstratingmore » a form of STTW well suited for MIMO environments. We implement STTW on the Coherent Logix hx3100 processor, a multicore processor intended for low-power, high-throughput software-defined signal processing. These results demonstrate how coupling the novel capabilities of emerging multicore processors with algorithmic advances can enable real-time, software-defined processing of large spatio-temporal data sets.« less

Modeling and Performance Considerations for Automated Fault Isolation in Complex Systems

NASA Technical Reports Server (NTRS)

Ferrell, Bob; Oostdyk, Rebecca

2010-01-01

The purpose of this paper is to document the modeling considerations and performance metrics that were examined in the development of a large-scale Fault Detection, Isolation and Recovery (FDIR) system. The FDIR system is envisioned to perform health management functions for both a launch vehicle and the ground systems that support the vehicle during checkout and launch countdown by using suite of complimentary software tools that alert operators to anomalies and failures in real-time. The FDIR team members developed a set of operational requirements for the models that would be used for fault isolation and worked closely with the vendor of the software tools selected for fault isolation to ensure that the software was able to meet the requirements. Once the requirements were established, example models of sufficient complexity were used to test the performance of the software. The results of the performance testing demonstrated the need for enhancements to the software in order to meet the demands of the full-scale ground and vehicle FDIR system. The paper highlights the importance of the development of operational requirements and preliminary performance testing as a strategy for identifying deficiencies in highly scalable systems and rectifying those deficiencies before they imperil the success of the project

Control software and electronics architecture design in the framework of the E-ELT instrumentation

NASA Astrophysics Data System (ADS)

Di Marcantonio, P.; Coretti, I.; Cirami, R.; Comari, M.; Santin, P.; Pucillo, M.

2010-07-01

During the last years the European Southern Observatory (ESO), in collaboration with other European astronomical institutes, has started several feasibility studies for the E-ELT (European-Extremely Large Telescope) instrumentation and post-focal adaptive optics. The goal is to create a flexible suite of instruments to deal with the wide variety of scientific questions astronomers would like to see solved in the coming decades. In this framework INAF-Astronomical Observatory of Trieste (INAF-AOTs) is currently responsible of carrying out the analysis and the preliminary study of the architecture of the electronics and control software of three instruments: CODEX (control software and electronics) and OPTIMOS-EVE/OPTIMOS-DIORAMAS (control software). To cope with the increased complexity and new requirements for stability, precision, real-time latency and communications among sub-systems imposed by these instruments, new solutions have been investigated by our group. In this paper we present the proposed software and electronics architecture based on a distributed common framework centered on the Component/Container model that uses OPC Unified Architecture as a standard layer to communicate with COTS components of three different vendors. We describe three working prototypes that have been set-up in our laboratory and discuss their performances, integration complexity and ease of deployment.

Reengineering legacy software to object-oriented systems

NASA Technical Reports Server (NTRS)

Pitman, C.; Braley, D.; Fridge, E.; Plumb, A.; Izygon, M.; Mears, B.

1994-01-01

NASA has a legacy of complex software systems that are becoming increasingly expensive to maintain. Reengineering is one approach to modemizing these systems. Object-oriented technology, other modem software engineering principles, and automated tools can be used to reengineer the systems and will help to keep maintenance costs of the modemized systems down. The Software Technology Branch at the NASA/Johnson Space Center has been developing and testing reengineering methods and tools for several years. The Software Technology Branch is currently providing training and consulting support to several large reengineering projects at JSC, including the Reusable Objects Software Environment (ROSE) project, which is reengineering the flight analysis and design system (over 2 million lines of FORTRAN code) into object-oriented C++. Many important lessons have been learned during the past years; one of these is that the design must never be allowed to diverge from the code during maintenance and enhancement. Future work on open, integrated environments to support reengineering is being actively planned.

Measuring the complexity of design in real-time imaging software

NASA Astrophysics Data System (ADS)

Sangwan, Raghvinder S.; Vercellone-Smith, Pamela; Laplante, Phillip A.

2007-02-01

Due to the intricacies in the algorithms involved, the design of imaging software is considered to be more complex than non-image processing software (Sangwan et al, 2005). A recent investigation (Larsson and Laplante, 2006) examined the complexity of several image processing and non-image processing software packages along a wide variety of metrics, including those postulated by McCabe (1976), Chidamber and Kemerer (1994), and Martin (2003). This work found that it was not always possible to quantitatively compare the complexity between imaging applications and nonimage processing systems. Newer research and an accompanying tool (Structure 101, 2006), however, provides a greatly simplified approach to measuring software complexity. Therefore it may be possible to definitively quantify the complexity differences between imaging and non-imaging software, between imaging and real-time imaging software, and between software programs of the same application type. In this paper, we review prior results and describe the methodology for measuring complexity in imaging systems. We then apply a new complexity measurement methodology to several sets of imaging and non-imaging code in order to compare the complexity differences between the two types of applications. The benefit of such quantification is far reaching, for example, leading to more easily measured performance improvement and quality in real-time imaging code.

Middleware Case Study: MeDICi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wynne, Adam S.

2011-05-05

In many application domains in science and engineering, data produced by sensors, instruments and networks is naturally processed by software applications structured as a pipeline . Pipelines comprise a sequence of software components that progressively process discrete units of data to produce a desired outcome. For example, in a Web crawler that is extracting semantics from text on Web sites, the first stage in the pipeline might be to remove all HTML tags to leave only the raw text of the document. The second step may parse the raw text to break it down into its constituent grammatical parts, suchmore » as nouns, verbs and so on. Subsequent steps may look for names of people or places, interesting events or times so documents can be sequenced on a time line. Each of these steps can be written as a specialized program that works in isolation with other steps in the pipeline. In many applications, simple linear software pipelines are sufficient. However, more complex applications require topologies that contain forks and joins, creating pipelines comprising branches where parallel execution is desirable. It is also increasingly common for pipelines to process very large files or high volume data streams which impose end-to-end performance constraints. Additionally, processes in a pipeline may have specific execution requirements and hence need to be distributed as services across a heterogeneous computing and data management infrastructure. From a software engineering perspective, these more complex pipelines become problematic to implement. While simple linear pipelines can be built using minimal infrastructure such as scripting languages, complex topologies and large, high volume data processing requires suitable abstractions, run-time infrastructures and development tools to construct pipelines with the desired qualities-of-service and flexibility to evolve to handle new requirements. The above summarizes the reasons we created the MeDICi Integration Framework (MIF) that is designed for creating high-performance, scalable and modifiable software pipelines. MIF exploits a low friction, robust, open source middleware platform and extends it with component and service-based programmatic interfaces that make implementing complex pipelines simple. The MIF run-time automatically handles queues between pipeline elements in order to handle request bursts, and automatically executes multiple instances of pipeline elements to increase pipeline throughput. Distributed pipeline elements are supported using a range of configurable communications protocols, and the MIF interfaces provide efficient mechanisms for moving data directly between two distributed pipeline elements.« less

The Design, Development and Testing of a Multi-process Real-time Software System

DTIC Science & Technology

2007-03-01

programming large systems stems from the complexity of dealing with many different details at one time. A sound engineering approach is to break...controls and 3) is portable to other OS platforms such as Microsoft Windows. Next, to reduce the complexity of the programming tasks, the system...processes depending on how often the process has to check to see if common data was modified. A good method for one process to quickly notify another

Ariadne's Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data.

PubMed

Nasso, Sara; Goetze, Sandra; Martens, Lennart

2015-09-04

Selected reaction monitoring (SRM) MS is a highly selective and sensitive technique to quantify protein abundances in complex biological samples. To enhance the pace of SRM large studies, a validated, robust method to fully automate absolute quantification and to substitute for interactive evaluation would be valuable. To address this demand, we present Ariadne, a Matlab software. To quantify monitored targets, Ariadne exploits metadata imported from the transition lists, and targets can be filtered according to mProphet output. Signal processing and statistical learning approaches are combined to compute peptide quantifications. To robustly estimate absolute abundances, the external calibration curve method is applied, ensuring linearity over the measured dynamic range. Ariadne was benchmarked against mProphet and Skyline by comparing its quantification performance on three different dilution series, featuring either noisy/smooth traces without background or smooth traces with complex background. Results, evaluated as efficiency, linearity, accuracy, and precision of quantification, showed that Ariadne's performance is independent of data smoothness and complex background presence and that Ariadne outperforms mProphet on the noisier data set and improved 2-fold Skyline's accuracy and precision for the lowest abundant dilution with complex background. Remarkably, Ariadne could statistically distinguish from each other all different abundances, discriminating dilutions as low as 0.1 and 0.2 fmol. These results suggest that Ariadne offers reliable and automated analysis of large-scale SRM differential expression studies.

Probabilistic Graphical Model Representation in Phylogenetics

PubMed Central

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

CRAX. Cassandra Exoskeleton

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, D.G.; Eubanks, L.

1998-03-01

This software assists the engineering designer in characterizing the statistical uncertainty in the performance of complex systems as a result of variations in manufacturing processes, material properties, system geometry or operating environment. The software is composed of a graphical user interface that provides the user with easy access to Cassandra uncertainty analysis routines. Together this interface and the Cassandra routines are referred to as CRAX (CassandRA eXoskeleton). The software is flexible enough, that with minor modification, it is able to interface with large modeling and analysis codes such as heat transfer or finite element analysis software. The current version permitsmore » the user to manually input a performance function, the number of random variables and their associated statistical characteristics: density function, mean, coefficients of variation. Additional uncertainity analysis modules are continuously being added to the Cassandra core.« less

Cassandra Exoskeleton

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robiinson, David G.

1999-02-20

This software assists the engineering designer in characterizing the statistical uncertainty in the performance of complex systems as a result of variations in manufacturing processes, material properties, system geometry or operating environment. The software is composed of a graphical user interface that provides the user with easy access to Cassandra uncertainty analysis routines. Together this interface and the Cassandra routines are referred to as CRAX (CassandRA eXoskeleton). The software is flexible enough, that with minor modification, it is able to interface with large modeling and analysis codes such as heat transfer or finite element analysis software. The current version permitsmore » the user to manually input a performance function, the number of random variables and their associated statistical characteristics: density function, mean, coefficients of variation. Additional uncertainity analysis modules are continuously being added to the Cassandra core.« less

Real-Time Extended Interface Automata for Software Testing Cases Generation

PubMed Central

Yang, Shunkun; Xu, Jiaqi; Man, Tianlong; Liu, Bin

2014-01-01

Testing and verification of the interface between software components are particularly important due to the large number of complex interactions, which requires the traditional modeling languages to overcome the existing shortcomings in the aspects of temporal information description and software testing input controlling. This paper presents the real-time extended interface automata (RTEIA) which adds clearer and more detailed temporal information description by the application of time words. We also establish the input interface automaton for every input in order to solve the problems of input controlling and interface covering nimbly when applied in the software testing field. Detailed definitions of the RTEIA and the testing cases generation algorithm are provided in this paper. The feasibility and efficiency of this method have been verified in the testing of one real aircraft braking system. PMID:24892080

The mathematical statement for the solving of the problem of N-version software system design

NASA Astrophysics Data System (ADS)

Kovalev, I. V.; Kovalev, D. I.; Zelenkov, P. V.; Voroshilova, A. A.

2015-10-01

The N-version programming, as a methodology of the fault-tolerant software systems design, allows successful solving of the mentioned tasks. The use of N-version programming approach turns out to be effective, since the system is constructed out of several parallel executed versions of some software module. Those versions are written to meet the same specification but by different programmers. The problem of developing an optimal structure of N-version software system presents a kind of very complex optimization problem. This causes the use of deterministic optimization methods inappropriate for solving the stated problem. In this view, exploiting heuristic strategies looks more rational. In the field of pseudo-Boolean optimization theory, the so called method of varied probabilities (MVP) has been developed to solve problems with a large dimensionality.

Overview of the TriBITS Lifecycle Model: Lean/Agile Software Lifecycle Model for Research-based Computational Science and Engineering Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartlett, Roscoe A; Heroux, Dr. Michael A; Willenbring, James

2012-01-01

Software lifecycles are becoming an increasingly important issue for computational science & engineering (CSE) software. The process by which a piece of CSE software begins life as a set of research requirements and then matures into a trusted high-quality capability is both commonplace and extremely challenging. Although an implicit lifecycle is obviously being used in any effort, the challenges of this process--respecting the competing needs of research vs. production--cannot be overstated. Here we describe a proposal for a well-defined software lifecycle process based on modern Lean/Agile software engineering principles. What we propose is appropriate for many CSE software projects thatmore » are initially heavily focused on research but also are expected to eventually produce usable high-quality capabilities. The model is related to TriBITS, a build, integration and testing system, which serves as a strong foundation for this lifecycle model, and aspects of this lifecycle model are ingrained in the TriBITS system. Indeed this lifecycle process, if followed, will enable large-scale sustainable integration of many complex CSE software efforts across several institutions.« less

The use of Tecnomatix software to simulate the manufacturing flows in an industrial enterprise producing hydrostatic components

NASA Astrophysics Data System (ADS)

Petrila, S.; Brabie, G.; Chirita, B.

2016-08-01

The analysis performed on manufacturing flows within industrial enterprises producing hydrostatic components twos made on a number of factors that influence smooth running of production such: distance between pieces, waiting time from one surgery to another; time achievement of setups on CNC machines; tool changing in case of a large number of operators and manufacturing complexity of large files [2]. To optimize the manufacturing flow it was used the software Tecnomatix. This software represents a complete portfolio of manufacturing solutions digital manufactured by Siemens. It provides innovation by linking all production methods of a product from process design, process simulation, validation and ending the manufacturing process. Among its many capabilities to create a wide range of simulations, the program offers various demonstrations regarding the behavior manufacturing cycles. This program allows the simulation and optimization of production systems and processes in several areas such as: car suppliers, production of industrial equipment; electronics manufacturing, design and production of aerospace and defense parts.

Complexity, Systems, and Software

DTIC Science & Technology

2014-08-14

2014 Carnegie Mellon University Complexity, Systems, and Software Software Engineering Institute Carnegie Mellon University Pittsburgh, PA...this collection of information, including suggestions for reducing this burden, to Washington Headquarters Services , Directorate for Information...OMB control number. 1. REPORT DATE 29 OCT 2014 2. REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE Complexity, Systems, and Software

Remote Sensing Image Analysis Without Expert Knowledge - A Web-Based Classification Tool On Top of Taverna Workflow Management System

NASA Astrophysics Data System (ADS)

Selsam, Peter; Schwartze, Christian

2016-10-01

Providing software solutions via internet has been known for quite some time and is now an increasing trend marketed as "software as a service". A lot of business units accept the new methods and streamlined IT strategies by offering web-based infrastructures for external software usage - but geospatial applications featuring very specialized services or functionalities on demand are still rare. Originally applied in desktop environments, the ILMSimage tool for remote sensing image analysis and classification was modified in its communicating structures and enabled for running on a high-power server and benefiting from Tavema software. On top, a GIS-like and web-based user interface guides the user through the different steps in ILMSimage. ILMSimage combines object oriented image segmentation with pattern recognition features. Basic image elements form a construction set to model for large image objects with diverse and complex appearance. There is no need for the user to set up detailed object definitions. Training is done by delineating one or more typical examples (templates) of the desired object using a simple vector polygon. The template can be large and does not need to be homogeneous. The template is completely independent from the segmentation. The object definition is done completely by the software.

Software Tools | Office of Cancer Clinical Proteomics Research

Cancer.gov

The CPTAC program develops new approaches to elucidate aspects of the molecular complexity of cancer made from large-scale proteogenomic datasets, and advance them toward precision medicine.  Part of the CPTAC mission is to make data and tools available and accessible to the greater research community to accelerate the discovery process.

Inventory-based landscape-scale simulation of management effectiveness and economic feasibility with BioSum

Treesearch

Jeremy S. Fried; Larry D. Potts; Sara M. Loreno; Glenn A. Christensen; R. Jamie Barbour

2017-01-01

The Forest Inventory and Analysis (FIA)-based BioSum (Bioregional Inventory Originated Simulation Under Management) is a free policy analysis framework and workflow management software solution. It addresses complex management questions concerning forest health and vulnerability for large, multimillion acre, multiowner landscapes using FIA plot data as the initial...

The Interaction between Multimedia Data Analysis and Theory Development in Design Research

ERIC Educational Resources Information Center

van Nes, Fenna; Doorman, Michiel

2010-01-01

Mathematics education researchers conducting instruction experiments using a design research methodology are challenged with the analysis of often complex and large amounts of qualitative data. In this paper, we present two case studies that show how multimedia analysis software can greatly support video data analysis and theory development in…

Software Surface Modeling and Grid Generation Steering Committee

NASA Technical Reports Server (NTRS)

Smith, Robert E. (Editor)

1992-01-01

It is a NASA objective to promote improvements in the capability and efficiency of computational fluid dynamics. Grid generation, the creation of a discrete representation of the solution domain, is an essential part of computational fluid dynamics. However, grid generation about complex boundaries requires sophisticated surface-model descriptions of the boundaries. The surface modeling and the associated computation of surface grids consume an extremely large percentage of the total time required for volume grid generation. Efficient and user friendly software systems for surface modeling and grid generation are critical for computational fluid dynamics to reach its potential. The papers presented here represent the state-of-the-art in software systems for surface modeling and grid generation. Several papers describe improved techniques for grid generation.

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

MrEnt: an editor for publication-quality phylogenetic tree illustrations.

PubMed

Zuccon, Alessandro; Zuccon, Dario

2014-09-01

We developed MrEnt, a Windows-based, user-friendly software that allows the production of complex, high-resolution, publication-quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication. © 2014 John Wiley & Sons Ltd.

DCL System Using Deep Learning Approaches for Land-based or Ship-based Real-Time Recognition and Localization of Marine Mammals

DTIC Science & Technology

2014-09-30

repeating pulse-like signals were investigated. Software prototypes were developed and integrated into distinct streams of reseach ; projects...to study complex sound archives spanning large spatial and temporal scales. A new post processing method for detection and classifcation was also...false positive rates. HK-ANN was successfully tested for a large minke whale dataset, but could easily be used on other signal types. Various

Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

This proposal develops scalable R / Bioconductor software infrastructure and data resources to integrate complex, heterogeneous, and large cancer genomic experiments. The falling cost of genomic assays facilitates collection of multiple data types (e.g., gene and transcript expression, structural variation, copy number, methylation, and microRNA data) from a set of clinical specimens. Furthermore, substantial resources are now available from large consortium activities like The Cancer Genome Atlas (TCGA).

The T.M.R. Data Dictionary: A Management Tool for Data Base Design

PubMed Central

Ostrowski, Maureen; Bernes, Marshall R.

1984-01-01

In January 1981, a dictionary-driven ambulatory care information system known as TMR (The Medical Record) was installed at a large private medical group practice in Los Angeles. TMR's data dictionary has enabled the medical group to adapt the software to meet changing user needs largely without programming support. For top management, the dictionary is also a tool for navigating through the system's complexity and assuring the integrity of management goals.

Efficient methods and readily customizable libraries for managing complexity of large networks.

PubMed

Dogrusoz, Ugur; Karacelik, Alper; Safarli, Ilkin; Balci, Hasan; Dervishi, Leonard; Siper, Metin Can

2018-01-01

One common problem in visualizing real-life networks, including biological pathways, is the large size of these networks. Often times, users find themselves facing slow, non-scaling operations due to network size, if not a "hairball" network, hindering effective analysis. One extremely useful method for reducing complexity of large networks is the use of hierarchical clustering and nesting, and applying expand-collapse operations on demand during analysis. Another such method is hiding currently unnecessary details, to later gradually reveal on demand. Major challenges when applying complexity reduction operations on large networks include efficiency and maintaining the user's mental map of the drawing. We developed specialized incremental layout methods for preserving a user's mental map while managing complexity of large networks through expand-collapse and hide-show operations. We also developed open-source JavaScript libraries as plug-ins to the web based graph visualization library named Cytsocape.js to implement these methods as complexity management operations. Through efficient specialized algorithms provided by these extensions, one can collapse or hide desired parts of a network, yielding potentially much smaller networks, making them more suitable for interactive visual analysis. This work fills an important gap by making efficient implementations of some already known complexity management techniques freely available to tool developers through a couple of open source, customizable software libraries, and by introducing some heuristics which can be applied upon such complexity management techniques to ensure preserving mental map of users.

The development and application of composite complexity models and a relative complexity metric in a software maintenance environment

NASA Technical Reports Server (NTRS)

Hops, J. M.; Sherif, J. S.

1994-01-01

A great deal of effort is now being devoted to the study, analysis, prediction, and minimization of software maintenance expected cost, long before software is delivered to users or customers. It has been estimated that, on the average, the effort spent on software maintenance is as costly as the effort spent on all other software costs. Software design methods should be the starting point to aid in alleviating the problems of software maintenance complexity and high costs. Two aspects of maintenance deserve attention: (1) protocols for locating and rectifying defects, and for ensuring that noe new defects are introduced in the development phase of the software process; and (2) protocols for modification, enhancement, and upgrading. This article focuses primarily on the second aspect, the development of protocols to help increase the quality and reduce the costs associated with modifications, enhancements, and upgrades of existing software. This study developed parsimonious models and a relative complexity metric for complexity measurement of software that were used to rank the modules in the system relative to one another. Some success was achieved in using the models and the relative metric to identify maintenance-prone modules.

Quantitative Measures for Software Independent Verification and Validation

NASA Technical Reports Server (NTRS)

Lee, Alice

1996-01-01

As software is maintained or reused, it undergoes an evolution which tends to increase the overall complexity of the code. To understand the effects of this, we brought in statistics experts and leading researchers in software complexity, reliability, and their interrelationships. These experts' project has resulted in our ability to statistically correlate specific code complexity attributes, in orthogonal domains, to errors found over time in the HAL/S flight software which flies in the Space Shuttle. Although only a prototype-tools experiment, the result of this research appears to be extendable to all other NASA software, given appropriate data similar to that logged for the Shuttle onboard software. Our research has demonstrated that a more complete domain coverage can be mathematically demonstrated with the approach we have applied, thereby ensuring full insight into the cause-and-effects relationship between the complexity of a software system and the fault density of that system. By applying the operational profile we can characterize the dynamic effects of software path complexity under this same approach We now have the ability to measure specific attributes which have been statistically demonstrated to correlate to increased error probability, and to know which actions to take, for each complexity domain. Shuttle software verifiers can now monitor the changes in the software complexity, assess the added or decreased risk of software faults in modified code, and determine necessary corrections. The reports, tool documentation, user's guides, and new approach that have resulted from this research effort represent advances in the state of the art of software quality and reliability assurance. Details describing how to apply this technique to other NASA code are contained in this document.

Queue and stack sorting algorithm optimization and performance analysis

NASA Astrophysics Data System (ADS)

Qian, Mingzhu; Wang, Xiaobao

2018-04-01

Sorting algorithm is one of the basic operation of a variety of software development, in data structures course specializes in all kinds of sort algorithm. The performance of the sorting algorithm is directly related to the efficiency of the software. A lot of excellent scientific research queue is constantly optimizing algorithm, algorithm efficiency better as far as possible, the author here further research queue combined with stacks of sorting algorithms, the algorithm is mainly used for alternating operation queue and stack storage properties, Thus avoiding the need for a large number of exchange or mobile operations in the traditional sort. Before the existing basis to continue research, improvement and optimization, the focus on the optimization of the time complexity of the proposed optimization and improvement, The experimental results show that the improved effectively, at the same time and the time complexity and space complexity of the algorithm, the stability study corresponding research. The improvement and optimization algorithm, improves the practicability.

Applications of Phase-Based Motion Processing

NASA Technical Reports Server (NTRS)

Branch, Nicholas A.; Stewart, Eric C.

2018-01-01

Image pyramids provide useful information in determining structural response at low cost using commercially available cameras. The current effort applies previous work on the complex steerable pyramid to analyze and identify imperceptible linear motions in video. Instead of implicitly computing motion spectra through phase analysis of the complex steerable pyramid and magnifying the associated motions, instead present a visual technique and the necessary software to display the phase changes of high frequency signals within video. The present technique quickly identifies regions of largest motion within a video with a single phase visualization and without the artifacts of motion magnification, but requires use of the computationally intensive Fourier transform. While Riesz pyramids present an alternative to the computationally intensive complex steerable pyramid for motion magnification, the Riesz formulation contains significant noise, and motion magnification still presents large amounts of data that cannot be quickly assessed by the human eye. Thus, user-friendly software is presented for quickly identifying structural response through optical flow and phase visualization in both Python and MATLAB.

MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.

PubMed

Martín-Campos, Trinidad; Mylonas, Roman; Masselot, Alexandre; Waridel, Patrice; Petricevic, Tanja; Xenarios, Ioannis; Quadroni, Manfredo

2017-08-04

Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTMs of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional investigation of PTMs on a protein of interest requires validation of the localization and the accurate quantitation of its changes across several conditions, tasks that often still require human evaluation. Software tools for large scale analyses are highly efficient but are rarely conceived for interactive, in-depth exploration of data on individual proteins. We here describe MsViz, a web-based and interactive software tool that supports manual validation of PTMs and their relative quantitation in small- and medium-size experiments. The tool displays sequence coverage information, peptide-spectrum matches, tandem MS spectra and extracted ion chromatograms through a single, highly intuitive interface. We found that MsViz greatly facilitates manual data inspection to validate PTM location and quantitate modified species across multiple samples.

Proposal for hierarchical description of software systems

NASA Technical Reports Server (NTRS)

Thauboth, H.

1973-01-01

The programming of digital computers has developed into a new dimension full of diffculties, because the hardware of computers has become so powerful that more complex applications are entrusted to computers. The costs of software development, verification, and maintenance are outpacing those of the hardware and the trend is toward futher increase of sophistication of application of computers and consequently of sophistication of software. To obtain better visibility into software systems and to improve the structure of software systems for better tests, verification, and maintenance, a clear, but rigorous description and documentation of software is needed. The purpose of the report is to extend the present methods in order to obtain a documentation that better reflects the interplay between the various components and functions of a software system at different levels of detail without losing the precision in expression. This is done by the use of block diagrams, sequence diagrams, and cross-reference charts. In the appendices, examples from an actual large sofware system, i.e. the Marshall System for Aerospace Systems Simulation (MARSYAS), are presented. The proposed documentation structure is compatible to automation of updating significant portions of the documentation for better software change control.

NASA Software Cost Estimation Model: An Analogy Based Estimation Model

NASA Technical Reports Server (NTRS)

Hihn, Jairus; Juster, Leora; Menzies, Tim; Mathew, George; Johnson, James

2015-01-01

The cost estimation of software development activities is increasingly critical for large scale integrated projects such as those at DOD and NASA especially as the software systems become larger and more complex. As an example MSL (Mars Scientific Laboratory) developed at the Jet Propulsion Laboratory launched with over 2 million lines of code making it the largest robotic spacecraft ever flown (Based on the size of the software). Software development activities are also notorious for their cost growth, with NASA flight software averaging over 50% cost growth. All across the agency, estimators and analysts are increasingly being tasked to develop reliable cost estimates in support of program planning and execution. While there has been extensive work on improving parametric methods there is very little focus on the use of models based on analogy and clustering algorithms. In this paper we summarize our findings on effort/cost model estimation and model development based on ten years of software effort estimation research using data mining and machine learning methods to develop estimation models based on analogy and clustering. The NASA Software Cost Model performance is evaluated by comparing it to COCOMO II, linear regression, and K-­ nearest neighbor prediction model performance on the same data set.

C++, objected-oriented programming, and astronomical data models

NASA Technical Reports Server (NTRS)

Farris, A.

1992-01-01

Contemporary astronomy is characterized by increasingly complex instruments and observational techniques, higher data collection rates, and large data archives, placing severe stress on software analysis systems. The object-oriented paradigm represents a significant new approach to software design and implementation that holds great promise for dealing with this increased complexity. The basic concepts of this approach will be characterized in contrast to more traditional procedure-oriented approaches. The fundamental features of objected-oriented programming will be discussed from a C++ programming language perspective, using examples familiar to astronomers. This discussion will focus on objects, classes and their relevance to the data type system; the principle of information hiding; and the use of inheritance to implement generalization/specialization relationships. Drawing on the object-oriented approach, features of a new database model to support astronomical data analysis will be presented.

Clinician user involvement in the real world: Designing an electronic tool to improve interprofessional communication and collaboration in a hospital setting.

PubMed

Tang, Terence; Lim, Morgan E; Mansfield, Elizabeth; McLachlan, Alexander; Quan, Sherman D

2018-02-01

User involvement is vital to the success of health information technology implementation. However, involving clinician users effectively and meaningfully in complex healthcare organizations remains challenging. The objective of this paper is to share our real-world experience of applying a variety of user involvement methods in the design and implementation of a clinical communication and collaboration platform aimed at facilitating care of complex hospitalized patients by an interprofessional team of clinicians. We designed and implemented an electronic clinical communication and collaboration platform in a large community teaching hospital. The design team consisted of both technical and healthcare professionals. Agile software development methodology was used to facilitate rapid iterative design and user input. We involved clinician users at all stages of the development lifecycle using a variety of user-centered, user co-design, and participatory design methods. Thirty-six software releases were delivered over 24 months. User involvement has resulted in improvement in user interface design, identification of software defects, creation of new modules that facilitated workflow, and identification of necessary changes to the scope of the project early on. A variety of user involvement methods were complementary and benefited the design and implementation of a complex health IT solution. Combining these methods with agile software development methodology can turn designs into functioning clinical system to support iterative improvement. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Software analysis handbook: Software complexity analysis and software reliability estimation and prediction

NASA Technical Reports Server (NTRS)

Lee, Alice T.; Gunn, Todd; Pham, Tuan; Ricaldi, Ron

1994-01-01

This handbook documents the three software analysis processes the Space Station Software Analysis team uses to assess space station software, including their backgrounds, theories, tools, and analysis procedures. Potential applications of these analysis results are also presented. The first section describes how software complexity analysis provides quantitative information on code, such as code structure and risk areas, throughout the software life cycle. Software complexity analysis allows an analyst to understand the software structure, identify critical software components, assess risk areas within a software system, identify testing deficiencies, and recommend program improvements. Performing this type of analysis during the early design phases of software development can positively affect the process, and may prevent later, much larger, difficulties. The second section describes how software reliability estimation and prediction analysis, or software reliability, provides a quantitative means to measure the probability of failure-free operation of a computer program, and describes the two tools used by JSC to determine failure rates and design tradeoffs between reliability, costs, performance, and schedule.

Software Engineering and Swarm-Based Systems

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Sterritt, Roy; Pena, Joaquin; Rouff, Christopher A.

2006-01-01

We discuss two software engineering aspects in the development of complex swarm-based systems. NASA researchers have been investigating various possible concept missions that would greatly advance future space exploration capabilities. The concept mission that we have focused on exploits the principles of autonomic computing as well as being based on the use of intelligent swarms, whereby a (potentially large) number of similar spacecraft collaborate to achieve mission goals. The intent is that such systems not only can be sent to explore remote and harsh environments but also are endowed with greater degrees of protection and longevity to achieve mission goals.

Viewpoints: A High-Performance High-Dimensional Exploratory Data Analysis Tool

NASA Astrophysics Data System (ADS)

Gazis, P. R.; Levit, C.; Way, M. J.

2010-12-01

Scientific data sets continue to increase in both size and complexity. In the past, dedicated graphics systems at supercomputing centers were required to visualize large data sets, but as the price of commodity graphics hardware has dropped and its capability has increased, it is now possible, in principle, to view large complex data sets on a single workstation. To do this in practice, an investigator will need software that is written to take advantage of the relevant graphics hardware. The Viewpoints visualization package described herein is an example of such software. Viewpoints is an interactive tool for exploratory visual analysis of large high-dimensional (multivariate) data. It leverages the capabilities of modern graphics boards (GPUs) to run on a single workstation or laptop. Viewpoints is minimalist: it attempts to do a small set of useful things very well (or at least very quickly) in comparison with similar packages today. Its basic feature set includes linked scatter plots with brushing, dynamic histograms, normalization, and outlier detection/removal. Viewpoints was originally designed for astrophysicists, but it has since been used in a variety of fields that range from astronomy, quantum chemistry, fluid dynamics, machine learning, bioinformatics, and finance to information technology server log mining. In this article, we describe the Viewpoints package and show examples of its usage.

Supporting metabolomics with adaptable software: design architectures for the end-user.

PubMed

Sarpe, Vladimir; Schriemer, David C

2017-02-01

Large and disparate sets of LC-MS data are generated by modern metabolomics profiling initiatives, and while useful software tools are available to annotate and quantify compounds, the field requires continued software development in order to sustain methodological innovation. Advances in software development practices allow for a new paradigm in tool development for metabolomics, where increasingly the end-user can develop or redeploy utilities ranging from simple algorithms to complex workflows. Resources that provide an organized framework for development are described and illustrated with LC-MS processing packages that have leveraged their design tools. Full access to these resources depends in part on coding experience, but the emergence of workflow builders and pluggable frameworks strongly reduces the skill level required. Developers in the metabolomics community are encouraged to use these resources and design content for uptake and reuse. Copyright © 2016 Elsevier Ltd. All rights reserved.

Stream Processors

NASA Astrophysics Data System (ADS)

Erez, Mattan; Dally, William J.

Stream processors, like other multi core architectures partition their functional units and storage into multiple processing elements. In contrast to typical architectures, which contain symmetric general-purpose cores and a cache hierarchy, stream processors have a significantly leaner design. Stream processors are specifically designed for the stream execution model, in which applications have large amounts of explicit parallel computation, structured and predictable control, and memory accesses that can be performed at a coarse granularity. Applications in the streaming model are expressed in a gather-compute-scatter form, yielding programs with explicit control over transferring data to and from on-chip memory. Relying on these characteristics, which are common to many media processing and scientific computing applications, stream architectures redefine the boundary between software and hardware responsibilities with software bearing much of the complexity required to manage concurrency, locality, and latency tolerance. Thus, stream processors have minimal control consisting of fetching medium- and coarse-grained instructions and executing them directly on the many ALUs. Moreover, the on-chip storage hierarchy of stream processors is under explicit software control, as is all communication, eliminating the need for complex reactive hardware mechanisms.

Probabilistic structural analysis methods for select space propulsion system components

NASA Technical Reports Server (NTRS)

Millwater, H. R.; Cruse, T. A.

1989-01-01

The Probabilistic Structural Analysis Methods (PSAM) project developed at the Southwest Research Institute integrates state-of-the-art structural analysis techniques with probability theory for the design and analysis of complex large-scale engineering structures. An advanced efficient software system (NESSUS) capable of performing complex probabilistic analysis has been developed. NESSUS contains a number of software components to perform probabilistic analysis of structures. These components include: an expert system, a probabilistic finite element code, a probabilistic boundary element code and a fast probability integrator. The NESSUS software system is shown. An expert system is included to capture and utilize PSAM knowledge and experience. NESSUS/EXPERT is an interactive menu-driven expert system that provides information to assist in the use of the probabilistic finite element code NESSUS/FEM and the fast probability integrator (FPI). The expert system menu structure is summarized. The NESSUS system contains a state-of-the-art nonlinear probabilistic finite element code, NESSUS/FEM, to determine the structural response and sensitivities. A broad range of analysis capabilities and an extensive element library is present.

The Influence of Software Complexity on the Maintenance Effort: Case Study on Software Developed within Educational Process

ERIC Educational Resources Information Center

Radulescu, Iulian Ionut

2006-01-01

Software complexity is the most important software quality attribute and a very useful instrument in the study of software quality. Is one of the factors that affect most of the software quality characteristics, including maintainability. It is very important to quantity this influence and identify the means to keep it under control; by using…

Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data.

PubMed

Teixeira, João M C; Skinner, Simon P; Arbesú, Miguel; Breeze, Alexander L; Pons, Miquel

2018-05-11

We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems' responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.

Measuring Business Process Learning with Enterprise Resource Planning Systems to Improve the Value of Education

ERIC Educational Resources Information Center

Monk, Ellen F.; Lycett, Mark

2016-01-01

Enterprise Resource Planning Systems (ERP) are very large and complex software packages that run every aspect of an organization. Increasingly, ERP systems are being used in higher education as one way to teach business processes, essential knowledge for students competing in today's business environment. Past research attempting to measure…

The software architecture to control the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Oya, I.; Füßling, M.; Antonino, P. O.; Conforti, V.; Hagge, L.; Melkumyan, D.; Morgenstern, A.; Tosti, G.; Schwanke, U.; Schwarz, J.; Wegner, P.; Colomé, J.; Lyard, E.

2016-07-01

The Cherenkov Telescope Array (CTA) project is an initiative to build two large arrays of Cherenkov gamma- ray telescopes. CTA will be deployed as two installations, one in the northern and the other in the southern hemisphere, containing dozens of telescopes of different sizes. CTA is a big step forward in the field of ground- based gamma-ray astronomy, not only because of the expected scientific return, but also due to the order-of- magnitude larger scale of the instrument to be controlled. The performance requirements associated with such a large and distributed astronomical installation require a thoughtful analysis to determine the best software solutions. The array control and data acquisition (ACTL) work-package within the CTA initiative will deliver the software to control and acquire the data from the CTA instrumentation. In this contribution we present the current status of the formal ACTL system decomposition into software building blocks and the relationships among them. The system is modelled via the Systems Modelling Language (SysML) formalism. To cope with the complexity of the system, this architecture model is sub-divided into different perspectives. The relationships with the stakeholders and external systems are used to create the first perspective, the context of the ACTL software system. Use cases are employed to describe the interaction of those external elements with the ACTL system and are traced to a hierarchy of functionalities (abstract system functions) describing the internal structure of the ACTL system. These functions are then traced to fully specified logical elements (software components), the deployment of which as technical elements, is also described. This modelling approach allows us to decompose the ACTL software in elements to be created and the ow of information within the system, providing us with a clear way to identify sub-system interdependencies. This architectural approach allows us to build the ACTL system model and trace requirements to deliverables (source code, documentation, etc.), and permits the implementation of a flexible use-case driven software development approach thanks to the traceability from use cases to the logical software elements. The Alma Common Software (ACS) container/component framework, used for the control of the Atacama Large Millimeter/submillimeter Array (ALMA) is the basis for the ACTL software and as such it is considered as an integral part of the software architecture.

Development of visual 3D virtual environment for control software

NASA Technical Reports Server (NTRS)

Hirose, Michitaka; Myoi, Takeshi; Amari, Haruo; Inamura, Kohei; Stark, Lawrence

1991-01-01

Virtual environments for software visualization may enable complex programs to be created and maintained. A typical application might be for control of regional electric power systems. As these encompass broader computer networks than ever, construction of such systems becomes very difficult. Conventional text-oriented environments are useful in programming individual processors. However, they are obviously insufficient to program a large and complicated system, that includes large numbers of computers connected to each other; such programming is called 'programming in the large.' As a solution for this problem, the authors are developing a graphic programming environment wherein one can visualize complicated software in virtual 3D world. One of the major features of the environment is the 3D representation of concurrent process. 3D representation is used to supply both network-wide interprocess programming capability (capability for 'programming in the large') and real-time programming capability. The authors' idea is to fuse both the block diagram (which is useful to check relationship among large number of processes or processors) and the time chart (which is useful to check precise timing for synchronization) into a single 3D space. The 3D representation gives us a capability for direct and intuitive planning or understanding of complicated relationship among many concurrent processes. To realize the 3D representation, a technology to enable easy handling of virtual 3D object is a definite necessity. Using a stereo display system and a gesture input device (VPL DataGlove), our prototype of the virtual workstation has been implemented. The workstation can supply the 'sensation' of the virtual 3D space to a programmer. Software for the 3D programming environment is implemented on the workstation. According to preliminary assessments, a 50 percent reduction of programming effort is achieved by using the virtual 3D environment. The authors expect that the 3D environment has considerable potential in the field of software engineering.

Parameters that affect parallel processing for computational electromagnetic simulation codes on high performance computing clusters

NASA Astrophysics Data System (ADS)

Moon, Hongsik

What is the impact of multicore and associated advanced technologies on computational software for science? Most researchers and students have multicore laptops or desktops for their research and they need computing power to run computational software packages. Computing power was initially derived from Central Processing Unit (CPU) clock speed. That changed when increases in clock speed became constrained by power requirements. Chip manufacturers turned to multicore CPU architectures and associated technological advancements to create the CPUs for the future. Most software applications benefited by the increased computing power the same way that increases in clock speed helped applications run faster. However, for Computational ElectroMagnetics (CEM) software developers, this change was not an obvious benefit - it appeared to be a detriment. Developers were challenged to find a way to correctly utilize the advancements in hardware so that their codes could benefit. The solution was parallelization and this dissertation details the investigation to address these challenges. Prior to multicore CPUs, advanced computer technologies were compared with the performance using benchmark software and the metric was FLoting-point Operations Per Seconds (FLOPS) which indicates system performance for scientific applications that make heavy use of floating-point calculations. Is FLOPS an effective metric for parallelized CEM simulation tools on new multicore system? Parallel CEM software needs to be benchmarked not only by FLOPS but also by the performance of other parameters related to type and utilization of the hardware, such as CPU, Random Access Memory (RAM), hard disk, network, etc. The codes need to be optimized for more than just FLOPs and new parameters must be included in benchmarking. In this dissertation, the parallel CEM software named High Order Basis Based Integral Equation Solver (HOBBIES) is introduced. This code was developed to address the needs of the changing computer hardware platforms in order to provide fast, accurate and efficient solutions to large, complex electromagnetic problems. The research in this dissertation proves that the performance of parallel code is intimately related to the configuration of the computer hardware and can be maximized for different hardware platforms. To benchmark and optimize the performance of parallel CEM software, a variety of large, complex projects are created and executed on a variety of computer platforms. The computer platforms used in this research are detailed in this dissertation. The projects run as benchmarks are also described in detail and results are presented. The parameters that affect parallel CEM software on High Performance Computing Clusters (HPCC) are investigated. This research demonstrates methods to maximize the performance of parallel CEM software code.

Enhancing E-Health Information Systems with Agent Technology

PubMed Central

Nguyen, Minh Tuan; Fuhrer, Patrik; Pasquier-Rocha, Jacques

2009-01-01

Agent Technology is an emerging and promising research area in software technology, which increasingly contributes to the development of value-added information systems for large healthcare organizations. Through the MediMAS prototype, resulting from a case study conducted at a local Swiss hospital, this paper aims at presenting the advantages of reinforcing such a complex E-health man-machine information organization with software agents. The latter will work on behalf of human agents, taking care of routine tasks, and thus increasing the speed, the systematic, and ultimately the reliability of the information exchanges. We further claim that the modeling of the software agent layer can be methodically derived from the actual “classical” laboratory organization and practices, as well as seamlessly integrated with the existing information system. PMID:19096509

Software Process Assessment (SPA)

NASA Technical Reports Server (NTRS)

Rosenberg, Linda H.; Sheppard, Sylvia B.; Butler, Scott A.

1994-01-01

NASA's environment mirrors the changes taking place in the nation at large, i.e. workers are being asked to do more work with fewer resources. For software developers at NASA's Goddard Space Flight Center (GSFC), the effects of this change are that we must continue to produce quality code that is maintainable and reusable, but we must learn to produce it more efficiently and less expensively. To accomplish this goal, the Data Systems Technology Division (DSTD) at GSFC is trying a variety of both proven and state-of-the-art techniques for software development (e.g., object-oriented design, prototyping, designing for reuse, etc.). In order to evaluate the effectiveness of these techniques, the Software Process Assessment (SPA) program was initiated. SPA was begun under the assumption that the effects of different software development processes, techniques, and tools, on the resulting product must be evaluated in an objective manner in order to assess any benefits that may have accrued. SPA involves the collection and analysis of software product and process data. These data include metrics such as effort, code changes, size, complexity, and code readability. This paper describes the SPA data collection and analysis methodology and presents examples of benefits realized thus far by DSTD's software developers and managers.

An expert system based software sizing tool, phase 2

NASA Technical Reports Server (NTRS)

Friedlander, David

1990-01-01

A software tool was developed for predicting the size of a future computer program at an early stage in its development. The system is intended to enable a user who is not expert in Software Engineering to estimate software size in lines of source code with an accuracy similar to that of an expert, based on the program's functional specifications. The project was planned as a knowledge based system with a field prototype as the goal of Phase 2 and a commercial system planned for Phase 3. The researchers used techniques from Artificial Intelligence and knowledge from human experts and existing software from NASA's COSMIC database. They devised a classification scheme for the software specifications, and a small set of generic software components that represent complexity and apply to large classes of programs. The specifications are converted to generic components by a set of rules and the generic components are input to a nonlinear sizing function which makes the final prediction. The system developed for this project predicted code sizes from the database with a bias factor of 1.06 and a fluctuation factor of 1.77, an accuracy similar to that of human experts but without their significant optimistic bias.

Python for large-scale electrophysiology.

PubMed

Spacek, Martin; Blanche, Tim; Swindale, Nicholas

2008-01-01

Electrophysiology is increasingly moving towards highly parallel recording techniques which generate large data sets. We record extracellularly in vivo in cat and rat visual cortex with 54-channel silicon polytrodes, under time-locked visual stimulation, from localized neuronal populations within a cortical column. To help deal with the complexity of generating and analysing these data, we used the Python programming language to develop three software projects: one for temporally precise visual stimulus generation ("dimstim"); one for electrophysiological waveform visualization and spike sorting ("spyke"); and one for spike train and stimulus analysis ("neuropy"). All three are open source and available for download (http://swindale.ecc.ubc.ca/code). The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three. Here we present our software as a showcase of the extensive capabilities of Python in neuroscience.

Variability extraction and modeling for product variants.

PubMed

Linsbauer, Lukas; Lopez-Herrejon, Roberto Erick; Egyed, Alexander

2017-01-01

Fast-changing hardware and software technologies in addition to larger and more specialized customer bases demand software tailored to meet very diverse requirements. Software development approaches that aim at capturing this diversity on a single consolidated platform often require large upfront investments, e.g., time or budget. Alternatively, companies resort to developing one variant of a software product at a time by reusing as much as possible from already-existing product variants. However, identifying and extracting the parts to reuse is an error-prone and inefficient task compounded by the typically large number of product variants. Hence, more disciplined and systematic approaches are needed to cope with the complexity of developing and maintaining sets of product variants. Such approaches require detailed information about the product variants, the features they provide and their relations. In this paper, we present an approach to extract such variability information from product variants. It identifies traces from features and feature interactions to their implementation artifacts, and computes their dependencies. This work can be useful in many scenarios ranging from ad hoc development approaches such as clone-and-own to systematic reuse approaches such as software product lines. We applied our variability extraction approach to six case studies and provide a detailed evaluation. The results show that the extracted variability information is consistent with the variability in our six case study systems given by their variability models and available product variants.

Photo-realistic Terrain Modeling and Visualization for Mars Exploration Rover Science Operations

NASA Technical Reports Server (NTRS)

Edwards, Laurence; Sims, Michael; Kunz, Clayton; Lees, David; Bowman, Judd

2005-01-01

Modern NASA planetary exploration missions employ complex systems of hardware and software managed by large teams of. engineers and scientists in order to study remote environments. The most complex and successful of these recent projects is the Mars Exploration Rover mission. The Computational Sciences Division at NASA Ames Research Center delivered a 30 visualization program, Viz, to the MER mission that provides an immersive, interactive environment for science analysis of the remote planetary surface. In addition, Ames provided the Athena Science Team with high-quality terrain reconstructions generated with the Ames Stereo-pipeline. The on-site support team for these software systems responded to unanticipated opportunities to generate 30 terrain models during the primary MER mission. This paper describes Viz, the Stereo-pipeline, and the experiences of the on-site team supporting the scientists at JPL during the primary MER mission.

Collaboration and decision making tools for mobile groups

NASA Astrophysics Data System (ADS)

Abrahamyan, Suren; Balyan, Serob; Ter-Minasyan, Harutyun; Degtyarev, Alexander

2017-12-01

Nowadays the use of distributed collaboration tools is widespread in many areas of people activity. But lack of mobility and certain equipment-dependency creates difficulties and decelerates development and integration of such technologies. Also mobile technologies allow individuals to interact with each other without need of traditional office spaces and regardless of location. Hence, realization of special infrastructures on mobile platforms with help of ad-hoc wireless local networks could eliminate hardware-attachment and be useful also in terms of scientific approach. Solutions from basic internet-messengers to complex software for online collaboration equipment in large-scale workgroups are implementations of tools based on mobile infrastructures. Despite growth of mobile infrastructures, applied distributed solutions in group decisionmaking and e-collaboration are not common. In this article we propose software complex for real-time collaboration and decision-making based on mobile devices, describe its architecture and evaluate performance.

Tessera: Open source software for accelerated data science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sego, Landon H.; Hafen, Ryan P.; Director, Hannah M.

2014-06-30

Extracting useful, actionable information from data can be a formidable challenge for the safeguards, nonproliferation, and arms control verification communities. Data scientists are often on the “front-lines” of making sense of complex and large datasets. They require flexible tools that make it easy to rapidly reformat large datasets, interactively explore and visualize data, develop statistical algorithms, and validate their approaches—and they need to perform these activities with minimal lines of code. Existing commercial software solutions often lack extensibility and the flexibility required to address the nuances of the demanding and dynamic environments where data scientists work. To address this need,more » Pacific Northwest National Laboratory developed Tessera, an open source software suite designed to enable data scientists to interactively perform their craft at the terabyte scale. Tessera automatically manages the complicated tasks of distributed storage and computation, empowering data scientists to do what they do best: tackling critical research and mission objectives by deriving insight from data. We illustrate the use of Tessera with an example analysis of computer network data.« less

The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.

PubMed

Gutman, David A; Khalilia, Mohammed; Lee, Sanghoon; Nalisnik, Michael; Mullen, Zach; Beezley, Jonathan; Chittajallu, Deepak R; Manthey, David; Cooper, Lee A D

2017-11-01

Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. In this article, we describe the Digital Slide Archive (DSA), an open-source web-based platform for digital pathology. DSA allows investigators to manage large collections of histologic images and integrate them with clinical and genomic metadata. The open-source model enables DSA to be extended to provide additional capabilities. Cancer Res; 77(21); e75-78. ©2017 AACR . ©2017 American Association for Cancer Research.

Designing for Change: Minimizing the Impact of Changing Requirements in the Later Stages of a Spaceflight Software Project

NASA Technical Reports Server (NTRS)

Allen, B. Danette

1998-01-01

In the traditional 'waterfall' model of the software project life cycle, the Requirements Phase ends and flows into the Design Phase, which ends and flows into the Development Phase. Unfortunately, the process rarely, if ever, works so smoothly in practice. Instead, software developers often receive new requirements, or modifications to the original requirements, well after the earlier project phases have been completed. In particular, projects with shorter than ideal schedules are highly susceptible to frequent requirements changes, as the software requirements analysis phase is often forced to begin before the overall system requirements and top-level design are complete. This results in later modifications to the software requirements, even though the software design and development phases may be complete. Requirements changes received in the later stages of a software project inevitably lead to modification of existing developed software. Presented here is a series of software design techniques that can greatly reduce the impact of last-minute requirements changes. These techniques were successfully used to add built-in flexibility to two complex software systems in which the requirements were expected to (and did) change frequently. These large, real-time systems were developed at NASA Langley Research Center (LaRC) to test and control the Lidar In-Space Technology Experiment (LITE) instrument which flew aboard the space shuttle Discovery as the primary payload on the STS-64 mission.

Viking Software Data

DTIC Science & Technology

1977-05-01

RADC-TR-77-168 Final Technical Report M~ay 1977 ll VIKING SOF11WARE DATA Martin Marietta Corporation Approved for public release; distribution...practices employed on a large and complex system development by the Martin Marietta Corporation. The intent of the RADC program to which this document...the technique are described. The preparation of this report could not have been accomplished without considerable assistance from fellow Martin

Instrument control software development process for the multi-star AO system ARGOS

NASA Astrophysics Data System (ADS)

Kulas, M.; Barl, L.; Borelli, J. L.; Gässler, W.; Rabien, S.

2012-09-01

The ARGOS project (Advanced Rayleigh guided Ground layer adaptive Optics System) will upgrade the Large Binocular Telescope (LBT) with an AO System consisting of six Rayleigh laser guide stars. This adaptive optics system integrates several control loops and many different components like lasers, calibration swing arms and slope computers that are dispersed throughout the telescope. The purpose of the instrument control software (ICS) is running this AO system and providing convenient client interfaces to the instruments and the control loops. The challenges for the ARGOS ICS are the development of a distributed and safety-critical software system with no defects in a short time, the creation of huge and complex software programs with a maintainable code base, the delivery of software components with the desired functionality and the support of geographically distributed project partners. To tackle these difficult tasks, the ARGOS software engineers reuse existing software like the novel middleware from LINC-NIRVANA, an instrument for the LBT, provide many tests at different functional levels like unit tests and regression tests, agree about code and architecture style and deliver software incrementally while closely collaborating with the project partners. Many ARGOS ICS components are already successfully in use in the laboratories for testing ARGOS control loops.

Data systems and computer science: Software Engineering Program

NASA Technical Reports Server (NTRS)

Zygielbaum, Arthur I.

1991-01-01

An external review of the Integrated Technology Plan for the Civil Space Program is presented. This review is specifically concerned with the Software Engineering Program. The goals of the Software Engineering Program are as follows: (1) improve NASA's ability to manage development, operation, and maintenance of complex software systems; (2) decrease NASA's cost and risk in engineering complex software systems; and (3) provide technology to assure safety and reliability of software in mission critical applications.

DnaSAM: Software to perform neutrality testing for large datasets with complex null models.

PubMed

Eckert, Andrew J; Liechty, John D; Tearse, Brandon R; Pande, Barnaly; Neale, David B

2010-05-01

Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file. © 2009 Blackwell Publishing Ltd.

Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data.

PubMed

Ralf, Arwin; Montiel González, Diego; Zhong, Kaiyin; Kayser, Manfred

2018-05-01

Next-generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y-chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy, and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data, it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods.

ChelomEx: Isotope-assisted discovery of metal chelates in complex media using high-resolution LC-MS.

PubMed

Baars, Oliver; Morel, François M M; Perlman, David H

2014-11-18

Chelating agents can control the speciation and reactivity of trace metals in biological, environmental, and laboratory-derived media. A large number of trace metals (including Fe, Cu, Zn, Hg, and others) show characteristic isotopic fingerprints that can be exploited for the discovery of known and unknown organic metal complexes and related chelating ligands in very complex sample matrices using high-resolution liquid chromatography mass spectrometry (LC-MS). However, there is currently no free open-source software available for this purpose. We present a novel software tool, ChelomEx, which identifies isotope pattern-matched chromatographic features associated with metal complexes along with free ligands and other related adducts in high-resolution LC-MS data. High sensitivity and exclusion of false positives are achieved by evaluation of the chromatographic coherence of the isotope pattern within chromatographic features, which we demonstrate through the analysis of bacterial culture media. A built-in graphical user interface and compound library aid in identification and efficient evaluation of results. ChelomEx is implemented in MatLab. The source code, binaries for MS Windows and MAC OS X as well as test LC-MS data are available for download at SourceForge ( http://sourceforge.net/projects/chelomex ).

Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics

NASA Astrophysics Data System (ADS)

Puzyrkov, Dmitry; Polyakov, Sergey; Podryga, Viktoriia; Markizov, Sergey

2018-02-01

At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.

PD5: a general purpose library for primer design software.

PubMed

Riley, Michael C; Aubrey, Wayne; Young, Michael; Clare, Amanda

2013-01-01

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications. The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C(++) with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification. The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design.

Coherent operation of detector systems and their readout electronics in a complex experiment control environment

NASA Astrophysics Data System (ADS)

Koestner, Stefan

2009-09-01

With the increasing size and degree of complexity of today's experiments in high energy physics the required amount of work and complexity to integrate a complete subdetector into an experiment control system is often underestimated. We report here on the layered software structure and protocols used by the LHCb experiment to control its detectors and readout boards. The experiment control system of LHCb is based on the commercial SCADA system PVSS II. Readout boards which are outside the radiation area are accessed via embedded credit card sized PCs which are connected to a large local area network. The SPECS protocol is used for control of the front end electronics. Finite state machines are introduced to facilitate the control of a large number of electronic devices and to model the whole experiment at the level of an expert system.

Tips on Creating Complex Geometry Using Solid Modeling Software

ERIC Educational Resources Information Center

Gow, George

2008-01-01

Three-dimensional computer-aided drafting (CAD) software, sometimes referred to as "solid modeling" software, is easy to learn, fun to use, and becoming the standard in industry. However, many users have difficulty creating complex geometry with the solid modeling software. And the problem is not entirely a student problem. Even some teachers and…

Collaboration Between NASA Centers of Excellence on Autonomous System Software Development

NASA Technical Reports Server (NTRS)

Goodrich, Charles H.; Larson, William E.; Delgado, H. (Technical Monitor)

2001-01-01

Software for space systems flight operations has its roots in the early days of the space program when computer systems were incapable of supporting highly complex and flexible control logic. Control systems relied on fast data acquisition and supervisory control from a roomful of systems engineers on the ground. Even though computer hardware and software has become many orders of magnitude more capable, space systems have largely adhered to this original paradigm In an effort to break this mold, Kennedy Space Center (KSC) has invested in the development of model-based diagnosis and control applications for ten years having broad experience in both ground and spacecraft systems and software. KSC has now partnered with Ames Research Center (ARC), NASA's Center of Excellence in Information Technology, to create a new paradigm for the control of dynamic space systems. ARC has developed model-based diagnosis and intelligent planning software that enables spacecraft to handle most routine problems automatically and allocate resources in a flexible way to realize mission objectives. ARC demonstrated the utility of onboard diagnosis and planning with an experiment aboard Deep Space I in 1999. This paper highlights the software control system collaboration between KSC and ARC. KSC has developed a Mars In-situ Resource Utilization testbed based on the Reverse Water Gas Shift (RWGS) reaction. This plant, built in KSC's Applied Chemistry Laboratory, is capable of producing the large amount of Oxygen that would be needed to support a Human Mars Mission. KSC and ARC are cooperating to develop an autonomous, fault-tolerant control system for RWGS to meet the need for autonomy on deep space missions. The paper will also describe how the new system software paradigm will be applied to Vehicle Health Monitoring, tested on the new X vehicles and integrated into future launch processing systems.

Los Alamos National Security, LLC Request for Information on how industry may partner with the Laboratory on KIVA software.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mcdonald, Kathleen Herrera

2016-02-29

KIVA is a family of Fortran-based computational fluid dynamics software developed by LANL. The software predicts complex fuel and air flows as well as ignition, combustion, and pollutant-formation processes in engines. The KIVA models have been used to understand combustion chemistry processes, such as auto-ignition of fuels, and to optimize diesel engines for high efficiency and low emissions. Fuel economy is heavily dependent upon engine efficiency, which in turn depends to a large degree on how fuel is burned within the cylinders of the engine. Higher in-cylinder pressures and temperatures lead to increased fuel economy, but they also create moremore » difficulty in controlling the combustion process. Poorly controlled and incomplete combustion can cause higher levels of emissions and lower engine efficiencies.« less

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

PubMed

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2016-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

Python for Large-Scale Electrophysiology

PubMed Central

Spacek, Martin; Blanche, Tim; Swindale, Nicholas

2008-01-01

Electrophysiology is increasingly moving towards highly parallel recording techniques which generate large data sets. We record extracellularly in vivo in cat and rat visual cortex with 54-channel silicon polytrodes, under time-locked visual stimulation, from localized neuronal populations within a cortical column. To help deal with the complexity of generating and analysing these data, we used the Python programming language to develop three software projects: one for temporally precise visual stimulus generation (“dimstim”); one for electrophysiological waveform visualization and spike sorting (“spyke”); and one for spike train and stimulus analysis (“neuropy”). All three are open source and available for download (http://swindale.ecc.ubc.ca/code). The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three. Here we present our software as a showcase of the extensive capabilities of Python in neuroscience. PMID:19198646

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

The role of artificial intelligence techniques in scheduling systems

NASA Technical Reports Server (NTRS)

Geoffroy, Amy L.; Britt, Daniel L.; Gohring, John R.

1990-01-01

Artificial Intelligence (AI) techniques provide good solutions for many of the problems which are characteristic of scheduling applications. However, scheduling is a large, complex heterogeneous problem. Different applications will require different solutions. Any individual application will require the use of a variety of techniques, including both AI and conventional software methods. The operational context of the scheduling system will also play a large role in design considerations. The key is to identify those places where a specific AI technique is in fact the preferable solution, and to integrate that technique into the overall architecture.

The environmental control and life support system advanced automation project. Phase 1: Application evaluation

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.

1990-01-01

The Environmental Control and Life Support System (ECLSS) is a Freedom Station distributed system with inherent applicability to advanced automation primarily due to the comparatively large reaction times of its subsystem processes. This allows longer contemplation times in which to form a more intelligent control strategy and to detect or prevent faults. The objective of the ECLSS Advanced Automation Project is to reduce the flight and ground manpower needed to support the initial and evolutionary ECLS system. The approach is to search out and make apparent those processes in the baseline system which are in need of more automatic control and fault detection strategies, to influence the ECLSS design by suggesting software hooks and hardware scars which will allow easy adaptation to advanced algorithms, and to develop complex software prototypes which fit into the ECLSS software architecture and will be shown in an ECLSS hardware testbed to increase the autonomy of the system. Covered here are the preliminary investigation and evaluation process, aimed at searching the ECLSS for candidate functions for automation and providing a software hooks and hardware scars analysis. This analysis shows changes needed in the baselined system for easy accommodation of knowledge-based or other complex implementations which, when integrated in flight or ground sustaining engineering architectures, will produce a more autonomous and fault tolerant Environmental Control and Life Support System.

Interoperable Acquisition for Systems of Systems: The Challenges

DTIC Science & Technology

2006-09-01

Interoperable Acquisition for Systems of Systems: The Challenges James D. Smith II D. Mike Phillips September 2006 TECHNICAL NOTE...Failure of Program-Centric Risk Management 10 3.3.2 Absence of System-of-Systems Engineering 12 3.3.3 Disconnect Between System-of-Systems...SOFTWARE ENGINEERING INSTITUTE | vii viii | CMU/SEI-2006-TN-034 Abstract Large, complex systems development has always been challenging , even when the

Building Safer Systems With SpecTRM

NASA Technical Reports Server (NTRS)

2003-01-01

System safety, an integral component in software development, often poses a challenge to engineers designing computer-based systems. While the relaxed constraints on software design allow for increased power and flexibility, this flexibility introduces more possibilities for error. As a result, system engineers must identify the design constraints necessary to maintain safety and ensure that the system and software design enforces them. Safeware Engineering Corporation, of Seattle, Washington, provides the information, tools, and techniques to accomplish this task with its Specification Tools and Requirements Methodology (SpecTRM). NASA assisted in developing this engineering toolset by awarding the company several Small Business Innovation Research (SBIR) contracts with Ames Research Center and Langley Research Center. The technology benefits NASA through its applications for Space Station rendezvous and docking. SpecTRM aids system and software engineers in developing specifications for large, complex safety critical systems. The product enables engineers to find errors early in development so that they can be fixed with the lowest cost and impact on the system design. SpecTRM traces both the requirements and design rationale (including safety constraints) throughout the system design and documentation, allowing engineers to build required system properties into the design from the beginning, rather than emphasizing assessment at the end of the development process when changes are limited and costly.System safety, an integral component in software development, often poses a challenge to engineers designing computer-based systems. While the relaxed constraints on software design allow for increased power and flexibility, this flexibility introduces more possibilities for error. As a result, system engineers must identify the design constraints necessary to maintain safety and ensure that the system and software design enforces them. Safeware Engineering Corporation, of Seattle, Washington, provides the information, tools, and techniques to accomplish this task with its Specification Tools and Requirements Methodology (SpecTRM). NASA assisted in developing this engineering toolset by awarding the company several Small Business Innovation Research (SBIR) contracts with Ames Research Center and Langley Research Center. The technology benefits NASA through its applications for Space Station rendezvous and docking. SpecTRM aids system and software engineers in developing specifications for large, complex safety critical systems. The product enables engineers to find errors early in development so that they can be fixed with the lowest cost and impact on the system design. SpecTRM traces both the requirements and design rationale (including safety constraints) throughout the system design and documentation, allowing engineers to build required system properties into the design from the beginning, rather than emphasizing assessment at the end of the development process when changes are limited and costly.

Digital geomorphological landslide hazard mapping of the Alpago area, Italy

NASA Astrophysics Data System (ADS)

van Westen, Cees J.; Soeters, Rob; Sijmons, Koert

Large-scale geomorphological maps of mountainous areas are traditionally made using complex symbol-based legends. They can serve as excellent "geomorphological databases", from which an experienced geomorphologist can extract a large amount of information for hazard mapping. However, these maps are not designed to be used in combination with a GIS, due to their complex cartographic structure. In this paper, two methods are presented for digital geomorphological mapping at large scales using GIS and digital cartographic software. The methods are applied to an area with a complex geomorphological setting on the Borsoia catchment, located in the Alpago region, near Belluno in the Italian Alps. The GIS database set-up is presented with an overview of the data layers that have been generated and how they are interrelated. The GIS database was also converted into a paper map, using a digital cartographic package. The resulting largescale geomorphological hazard map is attached. The resulting GIS database and cartographic product can be used to analyse the hazard type and hazard degree for each polygon, and to find the reasons for the hazard classification.

Engineering Complex Embedded Systems with State Analysis and the Mission Data System

NASA Technical Reports Server (NTRS)

Ingham, Michel D.; Rasmussen, Robert D.; Bennett, Matthew B.; Moncada, Alex C.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer s intent, potentially leading to software errors. This problem is addressed by a systems engineering methodology called State Analysis, which provides a process for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using State Analysis and how these requirements inform the design of the system software, using representative spacecraft examples.

Modeling software systems by domains

NASA Technical Reports Server (NTRS)

Dippolito, Richard; Lee, Kenneth

1992-01-01

The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

State analysis requirements database for engineering complex embedded systems

NASA Technical Reports Server (NTRS)

Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.

In-memory integration of existing software components for parallel adaptive unstructured mesh workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Cameron W.; Granzow, Brian; Diamond, Gerrett

Unstructured mesh methods, like finite elements and finite volumes, support the effective analysis of complex physical behaviors modeled by partial differential equations over general threedimensional domains. The most reliable and efficient methods apply adaptive procedures with a-posteriori error estimators that indicate where and how the mesh is to be modified. Although adaptive meshes can have two to three orders of magnitude fewer elements than a more uniform mesh for the same level of accuracy, there are many complex simulations where the meshes required are so large that they can only be solved on massively parallel systems.

In-memory integration of existing software components for parallel adaptive unstructured mesh workflows

DOE PAGES

Smith, Cameron W.; Granzow, Brian; Diamond, Gerrett; ...

2017-01-01

Unstructured mesh methods, like finite elements and finite volumes, support the effective analysis of complex physical behaviors modeled by partial differential equations over general threedimensional domains. The most reliable and efficient methods apply adaptive procedures with a-posteriori error estimators that indicate where and how the mesh is to be modified. Although adaptive meshes can have two to three orders of magnitude fewer elements than a more uniform mesh for the same level of accuracy, there are many complex simulations where the meshes required are so large that they can only be solved on massively parallel systems.

High throughput computing: a solution for scientific analysis

USGS Publications Warehouse

O'Donnell, M.

2011-01-01

handle job failures due to hardware, software, or network interruptions (obviating the need to manually resubmit the job after each stoppage); be affordable; and most importantly, allow us to complete very large, complex analyses that otherwise would not even be possible. In short, we envisioned a job-management system that would take advantage of unused FORT CPUs within a local area network (LAN) to effectively distribute and run highly complex analytical processes. What we found was a solution that uses High Throughput Computing (HTC) and High Performance Computing (HPC) systems to do exactly that (Figure 1).

Design and implementation of a software package to control a network of robotic observatories

NASA Astrophysics Data System (ADS)

Tuparev, G.; Nicolova, I.; Zlatanov, B.; Mihova, D.; Popova, I.; Hessman, F. V.

2006-09-01

We present a description of a reusable software package able to control a large, heterogeneous network of fully and semi-robotic observatories initially developed to run the MONET network of two 1.2 m telescopes. Special attention is given to the design of a robust, long-term observation scheduler which also allows the trading of observation time and facilities within various networks. The handling of the ``Phase I&II" project-development process, the time-accounting between complex organizational structures, and usability issues for making the package accessible not only to professional astronomers, but also to amateurs and high-school students is discussed. A simple RTML-based solution to link multiple networks is demonstrated.

A procedure for automated land use mapping using remotely sensed multispectral scanner data

NASA Technical Reports Server (NTRS)

Whitley, S. L.

1975-01-01

A system of processing remotely sensed multispectral scanner data by computer programs to produce color-coded land use maps for large areas is described. The procedure is explained, the software and the hardware are described, and an analogous example of the procedure is presented. Detailed descriptions of the multispectral scanners currently in use are provided together with a summary of the background of current land use mapping techniques. The data analysis system used in the procedure and the pattern recognition software used are functionally described. Current efforts by the NASA Earth Resources Laboratory to evaluate operationally a less complex and less costly system are discussed in a separate section.

Hierarchical Ada robot programming system (HARPS)- A complete and working telerobot control system based on the NASREM model

NASA Technical Reports Server (NTRS)

Leake, Stephen; Green, Tom; Cofer, Sue; Sauerwein, Tim

1989-01-01

HARPS is a telerobot control system that can perform some simple but useful tasks. This capability is demonstrated by performing the ORU exchange demonstration. HARPS is based on NASREM (NASA Standard Reference Model). All software is developed in Ada, and the project incorporates a number of different CASE (computer-aided software engineering) tools. NASREM was found to be a valid and useful model for building a telerobot control system. Its hierarchical and distributed structure creates a natural and logical flow for implementing large complex robust control systems. The ability of Ada to create and enforce abstraction enhanced the implementation of such control systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

pyLIMA: An Open-source Package for Microlensing Modeling. I. Presentation of the Software and Analysis of Single-lens Models

NASA Astrophysics Data System (ADS)

Bachelet, E.; Norbury, M.; Bozza, V.; Street, R.

2017-11-01

Microlensing is a unique tool, capable of detecting the “cold” planets between ˜1 and 10 au from their host stars and even unbound “free-floating” planets. This regime has been poorly sampled to date owing to the limitations of alternative planet-finding methods, but a watershed in discoveries is anticipated in the near future thanks to the planned microlensing surveys of WFIRST-AFTA and Euclid's Extended Mission. Of the many challenges inherent in these missions, the modeling of microlensing events will be of primary importance, yet it is often time-consuming, complex, and perceived as a daunting barrier to participation in the field. The large scale of future survey data products will require thorough but efficient modeling software, but, unlike other areas of exoplanet research, microlensing currently lacks a publicly available, well-documented package to conduct this type of analysis. We present version 1.0 of the python Lightcurve Identification and Microlensing Analysis (pyLIMA). This software is written in Python and uses existing packages as much as possible to make it widely accessible. In this paper, we describe the overall architecture of the software and the core modules for modeling single-lens events. To verify the performance of this software, we use it to model both real data sets from events published in the literature and generated test data produced using pyLIMA's simulation module. The results demonstrate that pyLIMA is an efficient tool for microlensing modeling. We will expand pyLIMA to consider more complex phenomena in the following papers.

Hierarchical storage of large volume of multidector CT data using distributed servers

NASA Astrophysics Data System (ADS)

Ratib, Osman; Rosset, Antoine; Heuberger, Joris; Bandon, David

2006-03-01

Multidector scanners and hybrid multimodality scanners have the ability to generate large number of high-resolution images resulting in very large data sets. In most cases, these datasets are generated for the sole purpose of generating secondary processed images and 3D rendered images as well as oblique and curved multiplanar reformatted images. It is therefore not essential to archive the original images after they have been processed. We have developed an architecture of distributed archive servers for temporary storage of large image datasets for 3D rendering and image processing without the need for long term storage in PACS archive. With the relatively low cost of storage devices it is possible to configure these servers to hold several months or even years of data, long enough for allowing subsequent re-processing if required by specific clinical situations. We tested the latest generation of RAID servers provided by Apple computers with a capacity of 5 TBytes. We implemented a peer-to-peer data access software based on our Open-Source image management software called OsiriX, allowing remote workstations to directly access DICOM image files located on the server through a new technology called "bonjour". This architecture offers a seamless integration of multiple servers and workstations without the need for central database or complex workflow management tools. It allows efficient access to image data from multiple workstation for image analysis and visualization without the need for image data transfer. It provides a convenient alternative to centralized PACS architecture while avoiding complex and time-consuming data transfer and storage.

A Software Tool for Integrated Optical Design Analysis

NASA Technical Reports Server (NTRS)

Moore, Jim; Troy, Ed; DePlachett, Charles; Montgomery, Edward (Technical Monitor)

2001-01-01

Design of large precision optical systems requires multi-disciplinary analysis, modeling, and design. Thermal, structural and optical characteristics of the hardware must be accurately understood in order to design a system capable of accomplishing the performance requirements. The interactions between each of the disciplines become stronger as systems are designed lighter weight for space applications. This coupling dictates a concurrent engineering design approach. In the past, integrated modeling tools have been developed that attempt to integrate all of the complex analysis within the framework of a single model. This often results in modeling simplifications and it requires engineering specialist to learn new applications. The software described in this presentation addresses the concurrent engineering task using a different approach. The software tool, Integrated Optical Design Analysis (IODA), uses data fusion technology to enable a cross discipline team of engineering experts to concurrently design an optical system using their standard validated engineering design tools.

A Java application for tissue section image analysis.

PubMed

Kamalov, R; Guillaud, M; Haskins, D; Harrison, A; Kemp, R; Chiu, D; Follen, M; MacAulay, C

2005-02-01

The medical industry has taken advantage of Java and Java technologies over the past few years, in large part due to the language's platform-independence and object-oriented structure. As such, Java provides powerful and effective tools for developing tissue section analysis software. The background and execution of this development are discussed in this publication. Object-oriented structure allows for the creation of "Slide", "Unit", and "Cell" objects to simulate the corresponding real-world objects. Different functions may then be created to perform various tasks on these objects, thus facilitating the development of the software package as a whole. At the current time, substantial parts of the initially planned functionality have been implemented. Getafics 1.0 is fully operational and currently supports a variety of research projects; however, there are certain features of the software that currently introduce unnecessary complexity and inefficiency. In the future, we hope to include features that obviate these problems.

KiT: a MATLAB package for kinetochore tracking.

PubMed

Armond, Jonathan W; Vladimirou, Elina; McAinsh, Andrew D; Burroughs, Nigel J

2016-06-15

During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present 'KiT' (Kinetochore Tracking)-an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization. KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development. Supplementary data are available at Bioinformatics online. jonathan.armond@warwick.ac.uk. © The Author 2016. Published by Oxford University Press.

Mapping Network Centric Operational Architectures to C2 and Software Architectures

DTIC Science & Technology

2007-06-01

Instead, the termite mound structure emerges as a result of the termites following very simple rules, and exchanging very simple pheromone signals...Each worker need make only fairly simple decisions.” For example, in far northern Australia, “magnetic termites ” build large termite mounds which are...oriented north-south and contain a complex ventilation system which controls temperature, humidity, and oxygen levels. But termite brains are too

An Open Service Provider Concept for Enterprise Complex Automation

NASA Astrophysics Data System (ADS)

Ivaschenko, A. V.; Sitnikov, P. V.; Tanonykhina, M. O.

2017-01-01

The paper introduces a solution for IT services representation and management in the integrated information space of distributed enterprises. It is proposed to develop an Open Service Provider as a software platform for interaction between IT services providers and their users. Implementation of the proposed concept and approach is illustrated by an after-sales customer support system for a large manufacturing corporation delivered by SEC “Open Code”.

The role of metrics and measurements in a software intensive total quality management environment

NASA Technical Reports Server (NTRS)

Daniels, Charles B.

1992-01-01

Paramax Space Systems began its mission as a member of the Rockwell Space Operations Company (RSOC) team which was the successful bidder on a massive operations consolidation contract for the Mission Operations Directorate (MOD) at JSC. The contract awarded to the team was the Space Transportation System Operations Contract (STSOC). Our initial challenge was to accept responsibility for a very large, highly complex and fragmented collection of software from eleven different contractors and transform it into a coherent, operational baseline. Concurrently, we had to integrate a diverse group of people from eleven different companies into a single, cohesive team. Paramax executives recognized the absolute necessity to develop a business culture based on the concept of employee involvement to execute and improve the complex process of our new environment. Our executives clearly understood that management needed to set the example and lead the way to quality improvement. The total quality management policy and the metrics used in this endeavor are presented.

Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

PubMed Central

Tinker, Nicholas A.; Bekele, Wubishet A.; Hattori, Jiro

2016-01-01

Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analyzing large data sets, applications of GBS may require substantial time, expertise, and computational resources. Haplotag, the novel GBS software described here, is freely available, and operates with minimal user-investment on widely available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode, and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; and (6) provides an intuitive visual “passport” for each inferred locus. Haplotag is optimized for use in a self-pollinating plant species. PMID:26818073

Toolboxes for a standardised and systematic study of glycans

PubMed Central

2014-01-01

Background Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics. PMID:24564482

Automated Theorem Proving in High-Quality Software Design

NASA Technical Reports Server (NTRS)

Schumann, Johann; Swanson, Keith (Technical Monitor)

2001-01-01

The amount and complexity of software developed during the last few years has increased tremendously. In particular, programs are being used more and more in embedded systems (from car-brakes to plant-control). Many of these applications are safety-relevant, i.e. a malfunction of hardware or software can cause severe damage or loss. Tremendous risks are typically present in the area of aviation, (nuclear) power plants or (chemical) plant control. Here, even small problems can lead to thousands of casualties and huge financial losses. Large financial risks also exist when computer systems are used in the area of telecommunication (telephone, electronic commerce) or space exploration. Computer applications in this area are not only subject to safety considerations, but also security issues are important. All these systems must be designed and developed to guarantee high quality with respect to safety and security. Even in an industrial setting which is (or at least should be) aware of the high requirements in Software Engineering, many incidents occur. For example, the Warshaw Airbus crash, was caused by an incomplete requirements specification. Uncontrolled reuse of an Ariane 4 software module was the reason for the Ariane 5 disaster. Some recent incidents in the telecommunication area, like illegal "cloning" of smart-cards of D2GSM handies, or the extraction of (secret) passwords from German T-online users show that also in this area serious flaws can happen. Due to the inherent complexity of computer systems, most authors claim that only a rigorous application of formal methods in all stages of the software life cycle can ensure high quality of the software and lead to real safe and secure systems. In this paper, we will have a look, in how far automated theorem proving can contribute to a more widespread application of formal methods and their tools, and what automated theorem provers (ATPs) must provide in order to be useful.

Hardware-Software Complex for Measurement of Energy and Angular Distributions of Charged Particles Formed in Nuclear Reactions

NASA Astrophysics Data System (ADS)

Vikhlyantsev, O. P.; Generalov, L. N.; Kuryakin, A. V.; Karpov, I. A.; Gurin, N. E.; Tumkin, A. D.; Fil'chagin, S. V.

2017-12-01

A hardware-software complex for measurement of energy and angular distributions of charged particles formed in nuclear reactions is presented. Hardware and software structures of the complex, the basic set of the modular nuclear-physical apparatus of a multichannel detecting system on the basis of Δ E- E telescopes of silicon detectors, and the hardware of experimental data collection, storage, and processing are presented and described.

Management Aspects of Software Maintenance.

DTIC Science & Technology

1984-09-01

educated in * the complex nature of software maintenance to be able to properly evaluate and manage the software maintenance effort. In this...maintenance and improvement may be called "software evolution". The soft- ware manager must be Educated in the complex nature cf soft- Iware maintenance to be...complaint of error or request for modification is also studied in order to determine what action needs tc be taken. 2. Define Objective and Approach :

Implementing Large Projects in Software Engineering Courses

ERIC Educational Resources Information Center

Coppit, David

2006-01-01

In software engineering education, large projects are widely recognized as a useful way of exposing students to the real-world difficulties of team software development. But large projects are difficult to put into practice. First, educators rarely have additional time to manage software projects. Second, classrooms have inherent limitations that…

Megatux

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-09-25

The Megatux platform enables the emulation of large scale (multi-million node) distributed systems. In particular, it allows for the emulation of large-scale networks interconnecting a very large number of emulated computer systems. It does this by leveraging virtualization and associated technologies to allow hundreds of virtual computers to be hosted on a single moderately sized server or workstation. Virtualization technology provided by modern processors allows for multiple guest OSs to run at the same time, sharing the hardware resources. The Megatux platform can be deployed on a single PC, a small cluster of a few boxes or a large clustermore » of computers. With a modest cluster, the Megatux platform can emulate complex organizational networks. By using virtualization, we emulate the hardware, but run actual software enabling large scale without sacrificing fidelity.« less

Observation-Driven Configuration of Complex Software Systems

NASA Astrophysics Data System (ADS)

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.

A META-COMPOSITE SOFTWARE DEVELOPMENT APPROACH FOR TRANSLATIONAL RESEARCH

PubMed Central

Sadasivam, Rajani S.; Tanik, Murat M.

2013-01-01

Translational researchers conduct research in a highly data-intensive and continuously changing environment and need to use multiple, disparate tools to achieve their goals. These researchers would greatly benefit from meta-composite software development or the ability to continuously compose and recompose tools together in response to their ever-changing needs. However, the available tools are largely disconnected, and current software approaches are inefficient and ineffective in their support for meta-composite software development. Building on the composite services development approach, the de facto standard for developing integrated software systems, we propose a concept-map and agent-based meta-composite software development approach. A crucial step in composite services development is the modeling of users’ needs as processes, which can then be specified in an executable format for system composition. We have two key innovations. First, our approach allows researchers (who understand their needs best) instead of technicians to take a leadership role in the development of process models, reducing inefficiencies and errors. A second innovation is that our approach also allows for modeling of complex user interactions as part of the process, overcoming the technical limitations of current tools. We demonstrate the feasibility of our approach using a real-world translational research use case. We also present results of usability studies evaluating our approach for future refinements. PMID:23504436

Advanced Automation for Ion Trap Mass Spectrometry-New Opportunities for Real-Time Autonomous Analysis

NASA Technical Reports Server (NTRS)

Palmer, Peter T.; Wong, C. M.; Salmonson, J. D.; Yost, R. A.; Griffin, T. P.; Yates, N. A.; Lawless, James G. (Technical Monitor)

1994-01-01

The utility of MS/MS for both target compound analysis and the structure elucidation of unknowns has been described in a number of references. A broader acceptance of this technique has not yet been realized as it requires large, complex, and costly instrumentation which has not been competitive with more conventional techniques. Recent advancements in ion trap mass spectrometry promise to change this situation. Although the ion trap's small size, sensitivity, and ability to perform multiple stages of mass spectrometry have made it eminently suitable for on-line, real-time monitoring applications, advance automation techniques are required to make these capabilities more accessible to non-experts. Towards this end we have developed custom software for the design and implementation of MS/MS experiments. This software allows the user to take full advantage of the ion trap's versatility with respect to ionization techniques, scan proxies, and ion accumulation/ejection methods. Additionally, expert system software has been developed for autonomous target compound analysis. This software has been linked to ion trap control software and a commercial data system to bring all of the steps in the analysis cycle under control of the expert system. These software development efforts and their utilization for a number of trace analysis applications will be described.

A meta-composite software development approach for translational research.

PubMed

Sadasivam, Rajani S; Tanik, Murat M

2013-06-01

Translational researchers conduct research in a highly data-intensive and continuously changing environment and need to use multiple, disparate tools to achieve their goals. These researchers would greatly benefit from meta-composite software development or the ability to continuously compose and recompose tools together in response to their ever-changing needs. However, the available tools are largely disconnected, and current software approaches are inefficient and ineffective in their support for meta-composite software development. Building on the composite services development approach, the de facto standard for developing integrated software systems, we propose a concept-map and agent-based meta-composite software development approach. A crucial step in composite services development is the modeling of users' needs as processes, which can then be specified in an executable format for system composition. We have two key innovations. First, our approach allows researchers (who understand their needs best) instead of technicians to take a leadership role in the development of process models, reducing inefficiencies and errors. A second innovation is that our approach also allows for modeling of complex user interactions as part of the process, overcoming the technical limitations of current tools. We demonstrate the feasibility of our approach using a real-world translational research use case. We also present results of usability studies evaluating our approach for future refinements.

MonALISA, an agent-based monitoring and control system for the LHC experiments

NASA Astrophysics Data System (ADS)

Balcas, J.; Kcira, D.; Mughal, A.; Newman, H.; Spiropulu, M.; Vlimant, J. R.

2017-10-01

MonALISA, which stands for Monitoring Agents using a Large Integrated Services Architecture, has been developed over the last fifteen years by California Insitute of Technology (Caltech) and its partners with the support of the software and computing program of the CMS and ALICE experiments at the Large Hadron Collider (LHC). The framework is based on Dynamic Distributed Service Architecture and is able to provide complete system monitoring, performance metrics of applications, Jobs or services, system control and global optimization services for complex systems. A short overview and status of MonALISA is given in this paper.

a Critical Review of Automated Photogrammetric Processing of Large Datasets

NASA Astrophysics Data System (ADS)

Remondino, F.; Nocerino, E.; Toschi, I.; Menna, F.

2017-08-01

The paper reports some comparisons between commercial software able to automatically process image datasets for 3D reconstruction purposes. The main aspects investigated in the work are the capability to correctly orient large sets of image of complex environments, the metric quality of the results, replicability and redundancy. Different datasets are employed, each one featuring a diverse number of images, GSDs at cm and mm resolutions, and ground truth information to perform statistical analyses of the 3D results. A summary of (photogrammetric) terms is also provided, in order to provide rigorous terms of reference for comparisons and critical analyses.

An Integrated Crustal Dynamics Simulator

NASA Astrophysics Data System (ADS)

Xing, H. L.; Mora, P.

2007-12-01

Numerical modelling offers an outstanding opportunity to gain an understanding of the crustal dynamics and complex crustal system behaviour. This presentation provides our long-term and ongoing effort on finite element based computational model and software development to simulate the interacting fault system for earthquake forecasting. A R-minimum strategy based finite-element computational model and software tool, PANDAS, for modelling 3-dimensional nonlinear frictional contact behaviour between multiple deformable bodies with the arbitrarily-shaped contact element strategy has been developed by the authors, which builds up a virtual laboratory to simulate interacting fault systems including crustal boundary conditions and various nonlinearities (e.g. from frictional contact, materials, geometry and thermal coupling). It has been successfully applied to large scale computing of the complex nonlinear phenomena in the non-continuum media involving the nonlinear frictional instability, multiple material properties and complex geometries on supercomputers, such as the South Australia (SA) interacting fault system, South California fault model and Sumatra subduction model. It has been also extended and to simulate the hot fractured rock (HFR) geothermal reservoir system in collaboration of Geodynamics Ltd which is constructing the first geothermal reservoir system in Australia and to model the tsunami generation induced by earthquakes. Both are supported by Australian Research Council.

Using VCL as an Aspect-Oriented Approach to Requirements Modelling

NASA Astrophysics Data System (ADS)

Amálio, Nuno; Kelsen, Pierre; Ma, Qin; Glodt, Christian

Software systems are becoming larger and more complex. By tackling the modularisation of crosscutting concerns, aspect orientation draws attention to modularity as a means to address the problems of scalability, complexity and evolution in software systems development. Aspect-oriented modelling (AOM) applies aspect-orientation to the construction of models. Most existing AOM approaches are designed without a formal semantics, and use multi-view partial descriptions of behaviour. This paper presents an AOM approach based on the Visual Contract Language (VCL): a visual language for abstract and precise modelling, designed with a formal semantics, and comprising a novel approach to visual behavioural modelling based on design by contract where behavioural descriptions are total. By applying VCL to a large case study of a car-crash crisis management system, the paper demonstrates how modularity of VCL's constructs, at different levels of granularity, help to tackle complexity. In particular, it shows how VCL's package construct and its associated composition mechanisms are key in supporting separation of concerns, coarse-grained problem decomposition and aspect-orientation. The case study's modelling solution has a clear and well-defined modular structure; the backbone of this structure is a collection of packages encapsulating local solutions to concerns.

Projected Impact of Compositional Verification on Current and Future Aviation Safety Risk

NASA Technical Reports Server (NTRS)

Reveley, Mary S.; Withrow, Colleen A.; Leone, Karen M.; Jones, Sharon M.

2014-01-01

The projected impact of compositional verification research conducted by the National Aeronautic and Space Administration System-Wide Safety and Assurance Technologies on aviation safety risk was assessed. Software and compositional verification was described. Traditional verification techniques have two major problems: testing at the prototype stage where error discovery can be quite costly and the inability to test for all potential interactions leaving some errors undetected until used by the end user. Increasingly complex and nondeterministic aviation systems are becoming too large for these tools to check and verify. Compositional verification is a "divide and conquer" solution to addressing increasingly larger and more complex systems. A review of compositional verification research being conducted by academia, industry, and Government agencies is provided. Forty-four aviation safety risks in the Biennial NextGen Safety Issues Survey were identified that could be impacted by compositional verification and grouped into five categories: automation design; system complexity; software, flight control, or equipment failure or malfunction; new technology or operations; and verification and validation. One capability, 1 research action, 5 operational improvements, and 13 enablers within the Federal Aviation Administration Joint Planning and Development Office Integrated Work Plan that could be addressed by compositional verification were identified.

Current Status of the High Contrast Imager for Complex Aperture Telescopes (HiCAT) Testbed

NASA Astrophysics Data System (ADS)

Brooks, Keira; Brady, Gregory; Brito, Arturo; Comeau, Tom; Dillon, Thomas; Choquet, Elodie; Egron, Sylvain; Rob, Gontrum; John, Hagopian; Leboulleux, Lucie; Perrin, Marshall; Petrone, Peter; Pueyo, Laurent; Mazoyer, Johan; Moriarty, Christopher; N’Diaye, Mamadou; Eldorado Riggs, A. J.; Shiri, Ron; Sivaramakrishnan, Anand; St. Laurent, Kathryn; Valenzuela, Ana Maria; Zimmerman, Neil; Soummer, Remi; JHU Mechanical Engineering Senior Design Team

2018-01-01

The coming decades will bring the next space telescopes to take on the ambitious goal of exoplanet discovery via direct imaging, driving the development of innovative coronagraphic solutions. High contrast imager for Complex Aperture Telescopes (HiCAT) is an optical testbed meant to test such solutions for complex aperture telescopes, such as the Large UV/Optical/InfraRed surveyor (LUVOIR), or any other segmented space observatory. High contrast imaging becomes more demanding with the addition of segments, a secondary mirror obscuration, and support structure. LUVOIR, a candidate for the next-next generation major space telescope funded in part by NASA, will have all three. In the past year, HiCAT has made significant hardware and software updates in order to meet the needs of LUVOIR. In addition to completely overhauling the software that runs the testbed, we have received the first two custom-made apodizers for the Apodized Pupil Lyot Coronagraph (APLC) that we are testing for LUVOIR, and are continuing the development of the wavefront sensing and control. This poster will serve to give an update on these, and other, changes, as well as the most recent results.

Shuttle mission simulator software conceptual design

NASA Technical Reports Server (NTRS)

Burke, J. F.

1973-01-01

Software conceptual designs (SCD) are presented for meeting the simulator requirements for the shuttle missions. The major areas of the SCD discussed include: malfunction insertion, flight software, applications software, systems software, and computer complex.

Personalized, Shareable Geoscience Dataspaces For Simplifying Data Management and Improving Reproducibility

NASA Astrophysics Data System (ADS)

Malik, T.; Foster, I.; Goodall, J. L.; Peckham, S. D.; Baker, J. B. H.; Gurnis, M.

2015-12-01

Research activities are iterative, collaborative, and now data- and compute-intensive. Such research activities mean that even the many researchers who work in small laboratories must often create, acquire, manage, and manipulate much diverse data and keep track of complex software. They face difficult data and software management challenges, and data sharing and reproducibility are neglected. There is signficant federal investment in powerful cyberinfrastructure, in part to lesson the burden associated with modern data- and compute-intensive research. Similarly, geoscience communities are establishing research repositories to facilitate data preservation. Yet we observe a large fraction of the geoscience community continues to struggle with data and software management. The reason, studies suggest, is not lack of awareness but rather that tools do not adequately support time-consuming data life cycle activities. Through NSF/EarthCube-funded GeoDataspace project, we are building personalized, shareable dataspaces that help scientists connect their individual or research group efforts with the community at large. The dataspaces provide a light-weight multiplatform research data management system with tools for recording research activities in what we call geounits, so that a geoscientist can at any time snapshot and preserve, both for their own use and to share with the community, all data and code required to understand and reproduce a study. A software-as-a-service (SaaS) deployment model enhances usability of core components, and integration with widely used software systems. In this talk we will present the open-source GeoDataspace project and demonstrate how it is enabling reproducibility across geoscience domains of hydrology, space science, and modeling toolkits.

OsiriX: an open-source software for navigating in multidimensional DICOM images.

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

Information Power Grid Posters

NASA Technical Reports Server (NTRS)

Vaziri, Arsi

2003-01-01

This document is a summary of the accomplishments of the Information Power Grid (IPG). Grids are an emerging technology that provide seamless and uniform access to the geographically dispersed, computational, data storage, networking, instruments, and software resources needed for solving large-scale scientific and engineering problems. The goal of the NASA IPG is to use NASA's remotely located computing and data system resources to build distributed systems that can address problems that are too large or complex for a single site. The accomplishments outlined in this poster presentation are: access to distributed data, IPG heterogeneous computing, integration of large-scale computing node into distributed environment, remote access to high data rate instruments,and exploratory grid environment.

Software Process Assurance for Complex Electronics

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Complex Electronics (CE) now perform tasks that were previously handled in software, such as communication protocols. Many methods used to develop software bare a close resemblance to CE development. Field Programmable Gate Arrays (FPGAs) can have over a million logic gates while system-on-chip (SOC) devices can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of software-like bugs such as incorrect design, logic, and unexpected interactions within the logic is great. With CE devices obscuring the hardware/software boundary, we propose that mature software methodologies may be utilized with slight modifications in the development of these devices. Software Process Assurance for Complex Electronics (SPACE) is a research project that used standardized S/W Assurance/Engineering practices to provide an assurance framework for development activities. Tools such as checklists, best practices and techniques were used to detect missing requirements and bugs earlier in the development cycle creating a development process for CE that was more easily maintained, consistent and configurable based on the device used.

The Development of Ada (Trademark) Software for Secure Environments

DTIC Science & Technology

1986-05-23

Telecommunications environment, This paper discusses software socurity and seeks to demostrate how the Ada programming language can be utilizec as a tool...complexity 4 . We use abstraction in our lives every day to control complexity; the principles of abstraction for software engineering are ro different...systems. These features directly sup,) )-t t.ie m odernp software engineering principles d1 s I , , 1 t, thne previous section. This is not surprising

Methodology of decreasing software complexity using ontology

NASA Astrophysics Data System (ADS)

DÄ browska-Kubik, Katarzyna

2015-09-01

In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

Software errors and complexity: An empirical investigation

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Perricone, Berry T.

1983-01-01

The distributions and relationships derived from the change data collected during the development of a medium scale satellite software project show that meaningful results can be obtained which allow an insight into software traits and the environment in which it is developed. Modified and new modules were shown to behave similarly. An abstract classification scheme for errors which allows a better understanding of the overall traits of a software project is also shown. Finally, various size and complexity metrics are examined with respect to errors detected within the software yielding some interesting results.

Software errors and complexity: An empirical investigation

NASA Technical Reports Server (NTRS)

Basili, V. R.; Perricone, B. T.

1982-01-01

The distributions and relationships derived from the change data collected during the development of a medium scale satellite software project show that meaningful results can be obtained which allow an insight into software traits and the environment in which it is developed. Modified and new modules were shown to behave similarly. An abstract classification scheme for errors which allows a better understanding of the overall traits of a software project is also shown. Finally, various size and complexity metrics are examined with respect to errors detected within the software yielding some interesting results.

Integrated Resource Planning Model (IRPM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, T. B.

2010-04-01

The Integrated Resource Planning Model (IRPM) is a decision-support software product for resource-and-capacity planning. Users can evaluate changing constraints on schedule performance, projected cost, and resource use. IRPM is a unique software tool that can analyze complex business situations from a basic supply chain to an integrated production facility to a distributed manufacturing complex. IRPM can be efficiently configured through a user-friendly graphical interface to rapidly provide charts, graphs, tables, and/or written results to summarize postulated business scenarios. There is not a similar integrated resource planning software package presently available. Many different businesses (from government to large corporations as wellmore » as medium-to-small manufacturing concerns) could save thousands of dollars and hundreds of labor hours in resource and schedule planning costs. Those businesses also could avoid millions of dollars of revenue lost from fear of overcommitting or from penalties and lost future business for failing to meet promised delivery by using IRPM to perform what-if business-case evaluations. Tough production planning questions that previously were left unanswered can now be answered with a high degree of certainty. Businesses can anticipate production problems and have solutions in hand to deal with those problems. IRPM allows companies to make better plans, decisions, and investments.« less

GPU Lossless Hyperspectral Data Compression System

NASA Technical Reports Server (NTRS)

Aranki, Nazeeh I.; Keymeulen, Didier; Kiely, Aaron B.; Klimesh, Matthew A.

2014-01-01

Hyperspectral imaging systems onboard aircraft or spacecraft can acquire large amounts of data, putting a strain on limited downlink and storage resources. Onboard data compression can mitigate this problem but may require a system capable of a high throughput. In order to achieve a high throughput with a software compressor, a graphics processing unit (GPU) implementation of a compressor was developed targeting the current state-of-the-art GPUs from NVIDIA(R). The implementation is based on the fast lossless (FL) compression algorithm reported in "Fast Lossless Compression of Multispectral-Image Data" (NPO- 42517), NASA Tech Briefs, Vol. 30, No. 8 (August 2006), page 26, which operates on hyperspectral data and achieves excellent compression performance while having low complexity. The FL compressor uses an adaptive filtering method and achieves state-of-the-art performance in both compression effectiveness and low complexity. The new Consultative Committee for Space Data Systems (CCSDS) Standard for Lossless Multispectral & Hyperspectral image compression (CCSDS 123) is based on the FL compressor. The software makes use of the highly-parallel processing capability of GPUs to achieve a throughput at least six times higher than that of a software implementation running on a single-core CPU. This implementation provides a practical real-time solution for compression of data from airborne hyperspectral instruments.

Predicting debris-flow initiation and run-out with a depth-averaged two-phase model and adaptive numerical methods

NASA Astrophysics Data System (ADS)

George, D. L.; Iverson, R. M.

2012-12-01

Numerically simulating debris-flow motion presents many challenges due to the complicated physics of flowing granular-fluid mixtures, the diversity of spatial scales (ranging from a characteristic particle size to the extent of the debris flow deposit), and the unpredictability of the flow domain prior to a simulation. Accurately predicting debris-flows requires models that are complex enough to represent the dominant effects of granular-fluid interaction, while remaining mathematically and computationally tractable. We have developed a two-phase depth-averaged mathematical model for debris-flow initiation and subsequent motion. Additionally, we have developed software that numerically solves the model equations efficiently on large domains. A unique feature of the mathematical model is that it includes the feedback between pore-fluid pressure and the evolution of the solid grain volume fraction, a process that regulates flow resistance. This feature endows the model with the ability to represent the transition from a stationary mass to a dynamic flow. With traditional approaches, slope stability analysis and flow simulation are treated separately, and the latter models are often initialized with force balances that are unrealistically far from equilibrium. Additionally, our new model relies on relatively few dimensionless parameters that are functions of well-known material properties constrained by physical data (eg. hydraulic permeability, pore-fluid viscosity, debris compressibility, Coulomb friction coefficient, etc.). We have developed numerical methods and software for accurately solving the model equations. By employing adaptive mesh refinement (AMR), the software can efficiently resolve an evolving debris flow as it advances through irregular topography, without needing terrain-fit computational meshes. The AMR algorithms utilize multiple levels of grid resolutions, so that computationally inexpensive coarse grids can be used where the flow is absent, and much higher resolution grids evolve with the flow. The reduction in computational cost, due to AMR, makes very large-scale problems tractable on personal computers. Model accuracy can be tested by comparison of numerical predictions and empirical data. These comparisons utilize controlled experiments conducted at the USGS debris-flow flume, which provide detailed data about flow mobilization and dynamics. Additionally, we have simulated historical large-scale debris flows, such as the (≈50 million m^3) debris flow that originated on Mt. Meager, British Columbia in 2010. This flow took a very complex route through highly variable topography and provides a valuable benchmark for testing. Maps of the debris flow deposit and data from seismic stations provide evidence regarding flow initiation, transit times and deposition. Our simulations reproduce many of the complex patterns of the event, such as run-out geometry and extent, and the large-scale nature of the flow and the complex topographical features demonstrate the utility of AMR in flow simulations.

Implementing Kanban for agile process management within the ALMA Software Operations Group

NASA Astrophysics Data System (ADS)

Reveco, Johnny; Mora, Matias; Shen, Tzu-Chiang; Soto, Ruben; Sepulveda, Jorge; Ibsen, Jorge

2014-07-01

After the inauguration of the Atacama Large Millimeter/submillimeter Array (ALMA), the Software Operations Group in Chile has refocused its objectives to: (1) providing software support to tasks related to System Integration, Scientific Commissioning and Verification, as well as Early Science observations; (2) testing the remaining software features, still under development by the Integrated Computing Team across the world; and (3) designing and developing processes to optimize and increase the level of automation of operational tasks. Due to their different stakeholders, each of these tasks presents a wide diversity of importances, lifespans and complexities. Aiming to provide the proper priority and traceability for every task without stressing our engineers, we introduced the Kanban methodology in our processes in order to balance the demand on the team against the throughput of the delivered work. The aim of this paper is to share experiences gained during the implementation of Kanban in our processes, describing the difficulties we have found, solutions and adaptations that led us to our current but still evolving implementation, which has greatly improved our throughput, prioritization and problem traceability.

Informatics in radiology (infoRAD): navigating the fifth dimension: innovative interface for multidimensional multimodality image navigation.

PubMed

Rosset, Antoine; Spadola, Luca; Pysher, Lance; Ratib, Osman

2006-01-01

The display and interpretation of images obtained by combining three-dimensional data acquired with two different modalities (eg, positron emission tomography and computed tomography) in the same subject require complex software tools that allow the user to adjust the image parameters. With the current fast imaging systems, it is possible to acquire dynamic images of the beating heart, which add a fourth dimension of visual information-the temporal dimension. Moreover, images acquired at different points during the transit of a contrast agent or during different functional phases add a fifth dimension-functional data. To facilitate real-time image navigation in the resultant large multidimensional image data sets, the authors developed a Digital Imaging and Communications in Medicine-compliant software program. The open-source software, called OsiriX, allows the user to navigate through multidimensional image series while adjusting the blending of images from different modalities, image contrast and intensity, and the rate of cine display of dynamic images. The software is available for free download at http://homepage.mac.com/rossetantoine/osirix. (c) RSNA, 2006.

The SCEC Broadband Platform: A Collaborative Open-Source Software Package for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Maechling, P. J.; Goulet, C.; Somerville, P.; Jordan, T. H.

2013-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform is a collaborative software development project involving SCEC researchers, graduate students, and the SCEC Community Modeling Environment. The SCEC Broadband Platform is open-source scientific software that can generate broadband (0-100Hz) ground motions for earthquakes, integrating complex scientific modules that implement rupture generation, low and high-frequency seismogram synthesis, non-linear site effects calculation, and visualization into a software system that supports easy on-demand computation of seismograms. The Broadband Platform operates in two primary modes: validation simulations and scenario simulations. In validation mode, the Broadband Platform runs earthquake rupture and wave propagation modeling software to calculate seismograms of a historical earthquake for which observed strong ground motion data is available. Also in validation mode, the Broadband Platform calculates a number of goodness of fit measurements that quantify how well the model-based broadband seismograms match the observed seismograms for a certain event. Based on these results, the Platform can be used to tune and validate different numerical modeling techniques. During the past year, we have modified the software to enable the addition of a large number of historical events, and we are now adding validation simulation inputs and observational data for 23 historical events covering the Eastern and Western United States, Japan, Taiwan, Turkey, and Italy. In scenario mode, the Broadband Platform can run simulations for hypothetical (scenario) earthquakes. In this mode, users input an earthquake description, a list of station names and locations, and a 1D velocity model for their region of interest, and the Broadband Platform software then calculates ground motions for the specified stations. By establishing an interface between scientific modules with a common set of input and output files, the Broadband Platform facilitates the addition of new scientific methods, which are written by earth scientists in a number of languages such as C, C++, Fortran, and Python. The Broadband Platform's modular design also supports the reuse of existing software modules as building blocks to create new scientific methods. Additionally, the Platform implements a wrapper around each scientific module, converting input and output files to and from the specific formats required (or produced) by individual scientific codes. Working in close collaboration with scientists and research engineers, the SCEC software development group continues to add new capabilities to the Broadband Platform and to release new versions as open-source scientific software distributions that can be compiled and run on many Linux computer systems. Our latest release includes the addition of 3 new simulation methods and several new data products, such as map and distance-based goodness of fit plots. Finally, as the number and complexity of scenarios simulated using the Broadband Platform increase, we have added batching utilities to substantially improve support for running large-scale simulations on computing clusters.

A virtual reality environment for telescope operation

NASA Astrophysics Data System (ADS)

Martínez, Luis A.; Villarreal, José L.; Ángeles, Fernando; Bernal, Abel

2010-07-01

Astronomical observatories and telescopes are becoming increasingly large and complex systems, demanding to any potential user the acquirement of great amount of information previous to access them. At present, the most common way to overcome that information is through the implementation of larger graphical user interfaces and computer monitors to increase the display area. Tonantzintla Observatory has a 1-m telescope with a remote observing system. As a step forward in the improvement of the telescope software, we have designed a Virtual Reality (VR) environment that works as an extension of the remote system and allows us to operate the telescope. In this work we explore this alternative technology that is being suggested here as a software platform for the operation of the 1-m telescope.

Operations management system

NASA Technical Reports Server (NTRS)

Brandli, A. E.; Eckelkamp, R. E.; Kelly, C. M.; Mccandless, W.; Rue, D. L.

1990-01-01

The objective of an operations management system is to provide an orderly and efficient method to operate and maintain aerospace vehicles. Concepts are described for an operations management system and the key technologies are highlighted which will be required if this capability is brought to fruition. Without this automation and decision aiding capability, the growing complexity of avionics will result in an unmanageable workload for the operator, ultimately threatening mission success or survivability of the aircraft or space system. The key technologies include expert system application to operational tasks such as replanning, equipment diagnostics and checkout, global system management, and advanced man machine interfaces. The economical development of operations management systems, which are largely software, will require advancements in other technological areas such as software engineering and computer hardware.

The pseudo-Boolean optimization approach to form the N-version software structure

NASA Astrophysics Data System (ADS)

Kovalev, I. V.; Kovalev, D. I.; Zelenkov, P. V.; Voroshilova, A. A.

2015-10-01

The problem of developing an optimal structure of N-version software system presents a kind of very complex optimization problem. This causes the use of deterministic optimization methods inappropriate for solving the stated problem. In this view, exploiting heuristic strategies looks more rational. In the field of pseudo-Boolean optimization theory, the so called method of varied probabilities (MVP) has been developed to solve problems with a large dimensionality. Some additional modifications of MVP have been made to solve the problem of N-version systems design. Those algorithms take into account the discovered specific features of the objective function. The practical experiments have shown the advantage of using these algorithm modifications because of reducing a search space.

Fast assembling of neuron fragments in serial 3D sections.

PubMed

Chen, Hanbo; Iascone, Daniel Maxim; da Costa, Nuno Maçarico; Lein, Ed S; Liu, Tianming; Peng, Hanchuan

2017-09-01

Reconstructing neurons from 3D image-stacks of serial sections of thick brain tissue is very time-consuming and often becomes a bottleneck in high-throughput brain mapping projects. We developed NeuronStitcher, a software suite for stitching non-overlapping neuron fragments reconstructed in serial 3D image sections. With its efficient algorithm and user-friendly interface, NeuronStitcher has been used successfully to reconstruct very large and complex human and mouse neurons.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

PubMed Central

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2017-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

Thermal modeling and analysis of structurally complex spacecraft using the IDEAS system

NASA Technical Reports Server (NTRS)

Garrett, L. B.

1983-01-01

Large antenna satellites of unprecedented sizes are needed for a number of applications. Antenna diameters on the order of 50 meters and upward are required. Such antennas involve the use of large expanses of lattice structures with hundreds or thousands of individual connecting members. In connection with the design of such structures, the consideration of thermal effects represents a crucial factor. Software capabilities have emerged which are coded to include major first order thermal effects and to purposely ignore, in the interest of computational efficiency, the secondary effects. The Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) is one such system. It has been developed for an employment in connection with thermal-structural interaction analyses related to the design of large structurally complex classes of future spacecraft. An IDEAS overview is presented. Attention is given to a typical antenna analysis using IDEAS, the thermal and loading analyses of a tetrahedral truss spacecraft, and ecliptic and polar orbit analyses.

Editorial [Special issue on software defined networks and infrastructures, network function virtualisation, autonomous systems and network management

DOE PAGES

Biswas, Amitava; Liu, Chen; Monga, Inder; ...

2016-01-01

For last few years, there has been a tremendous growth in data traffic due to high adoption rate of mobile devices and cloud computing. Internet of things (IoT) will stimulate even further growth. This is increasing scale and complexity of telecom/internet service provider (SP) and enterprise data centre (DC) compute and network infrastructures. As a result, managing these large network-compute converged infrastructures is becoming complex and cumbersome. To cope up, network and DC operators are trying to automate network and system operations, administrations and management (OAM) functions. OAM includes all non-functional mechanisms which keep the network running.

OpenSoC Fabric

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-08-21

Recent advancements in technology scaling have shown a trend towards greater integration with large-scale chips containing thousands of processors connected to memories and other I/O devices using non-trivial network topologies. Software simulation proves insufficient to study the tradeoffs in such complex systems due to slow execution time, whereas hardware RTL development is too time-consuming. We present OpenSoC Fabric, an on-chip network generation infrastructure which aims to provide a parameterizable and powerful on-chip network generator for evaluating future high performance computing architectures based on SoC technology. OpenSoC Fabric leverages a new hardware DSL, Chisel, which contains powerful abstractions provided by itsmore » base language, Scala, and generates both software (C++) and hardware (Verilog) models from a single code base. The OpenSoC Fabric2 infrastructure is modeled after existing state-of-the-art simulators, offers large and powerful collections of configuration options, and follows object-oriented design and functional programming to make functionality extension as easy as possible.« less

A feasible injection molding technique for the manufacturing of large diameter aspheric plastic lenses

NASA Astrophysics Data System (ADS)

Shieh, Jen-Yu; Wang, Luke K.; Ke, Shih-Ying

2010-07-01

A computer aided engineering (CAE) tool-assisted technique, using Moldex3D and aspheric analysis utility (AAU) software in a polycarbonate injection molding design, is proposed to manufacture large diameter aspheric plastic lenses. An experiment is conducted to verify the applicability/feasibility of the proposed technique. Using the preceding two software tools, these crucial process parameters associated with the surface profile errors and birefringence of a molded lens can be attainable. The strategy adopted here is to use the actual quantity of shrinkage after an injection molding trial of an aspherical plastic lens as a reference to perform the core shaping job while keeping the coefficients of aspheric surface, radius, and conic constant unchanged. The design philosophy is characterized by using the CAE tool as a guideline to pursue the best symmetry condition, followed by injection molding trials, to accelerate a product’s developmental time. The advantages are less design complexity and shorter developmental time for a product.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Lecocq, Thomas; Megies, Tobias; Krischer, Lion; Sales de Andrade, Elliott; Barsch, Robert; Beyreuther, Moritz

2016-04-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides * read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, * a comprehensive signal processing toolbox tuned to the needs of seismologists, * integrated access to all large data centers, web services and databases, and * convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software. ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. This contribution will give a short introduction and overview of ObsPy and highlight a number of use cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; Beyreuther, M.

2015-12-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, a comprehensive signal processing toolbox tuned to the needs of seismologists, integrated access to all large data centers, web services and databases, and convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software.ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it.This contribution will give a short introduction and overview of ObsPy and highlight a number of us cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

Critical evaluation of reverse engineering tool Imagix 4D!

PubMed

Yadav, Rashmi; Patel, Ravindra; Kothari, Abhay

2016-01-01

The comprehension of legacy codes is difficult to understand. Various commercial reengineering tools are available that have unique working styles, and are equipped with their inherent capabilities and shortcomings. The focus of the available tools is in visualizing static behavior not the dynamic one. Therefore, it is difficult for people who work in software product maintenance, code understanding reengineering/reverse engineering. Consequently, the need for a comprehensive reengineering/reverse engineering tool arises. We found the usage of Imagix 4D to be good as it generates the maximum pictorial representations in the form of flow charts, flow graphs, class diagrams, metrics and, to a partial extent, dynamic visualizations. We evaluated Imagix 4D with the help of a case study involving a few samples of source code. The behavior of the tool was analyzed on multiple small codes and a large code gcc C parser. Large code evaluation was performed to uncover dead code, unstructured code, and the effect of not including required files at preprocessing level. The utility of Imagix 4D to prepare decision density and complexity metrics for a large code was found to be useful in getting to know how much reengineering is required. At the outset, Imagix 4D offered limitations in dynamic visualizations, flow chart separation (large code) and parsing loops. The outcome of evaluation will eventually help in upgrading Imagix 4D and posed a need of full featured tools in the area of software reengineering/reverse engineering. It will also help the research community, especially those who are interested in the realm of software reengineering tool building.

The SCEC Broadband Platform: A Collaborative Open-Source Software Package for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Maechling, P. J.; Goulet, C. A.; Somerville, P.; Jordan, T. H.

2014-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform is a collaborative software development project involving geoscientists, earthquake engineers, graduate students, and the SCEC Community Modeling Environment. The SCEC Broadband Platform (BBP) is open-source scientific software that can generate broadband (0-100Hz) ground motions for earthquakes, integrating complex scientific modules that implement rupture generation, low and high-frequency seismogram synthesis, non-linear site effects calculation, and visualization into a software system that supports easy on-demand computation of seismograms. The Broadband Platform operates in two primary modes: validation simulations and scenario simulations. In validation mode, the Platform runs earthquake rupture and wave propagation modeling software to calculate seismograms for a well-observed historical earthquake. Then, the BBP calculates a number of goodness of fit measurements that quantify how well the model-based broadband seismograms match the observed seismograms for a certain event. Based on these results, the Platform can be used to tune and validate different numerical modeling techniques. In scenario mode, the Broadband Platform can run simulations for hypothetical (scenario) earthquakes. In this mode, users input an earthquake description, a list of station names and locations, and a 1D velocity model for their region of interest, and the Broadband Platform software then calculates ground motions for the specified stations. Working in close collaboration with scientists and research engineers, the SCEC software development group continues to add new capabilities to the Broadband Platform and to release new versions as open-source scientific software distributions that can be compiled and run on many Linux computer systems. Our latest release includes 5 simulation methods, 7 simulation regions covering California, Japan, and Eastern North America, the ability to compare simulation results against GMPEs, and several new data products, such as map and distance-based goodness of fit plots. As the number and complexity of scenarios simulated using the Broadband Platform increases, we have added batching utilities to substantially improve support for running large-scale simulations on computing clusters.

Development of simulation computer complex specification

NASA Technical Reports Server (NTRS)

1973-01-01

The Training Simulation Computer Complex Study was one of three studies contracted in support of preparations for procurement of a shuttle mission simulator for shuttle crew training. The subject study was concerned with definition of the software loads to be imposed on the computer complex to be associated with the shuttle mission simulator and the development of procurement specifications based on the resulting computer requirements. These procurement specifications cover the computer hardware and system software as well as the data conversion equipment required to interface the computer to the simulator hardware. The development of the necessary hardware and software specifications required the execution of a number of related tasks which included, (1) simulation software sizing, (2) computer requirements definition, (3) data conversion equipment requirements definition, (4) system software requirements definition, (5) a simulation management plan, (6) a background survey, and (7) preparation of the specifications.

Configurable software for satellite graphics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartzman, P D

An important goal in interactive computer graphics is to provide users with both quick system responses for basic graphics functions and enough computing power for complex calculations. One solution is to have a distributed graphics system in which a minicomputer and a powerful large computer share the work. The most versatile type of distributed system is an intelligent satellite system in which the minicomputer is programmable by the application user and can do most of the work while the large remote machine is used for difficult computations. At New York University, the hardware was configured from available equipment. The levelmore » of system intelligence resulted almost completely from software development. Unlike previous work with intelligent satellites, the resulting system had system control centered in the satellite. It also had the ability to reconfigure software during realtime operation. The design of the system was done at a very high level using set theoretic language. The specification clearly illustrated processor boundaries and interfaces. The high-level specification also produced a compact, machine-independent virtual graphics data structure for picture representation. The software was written in a systems implementation language; thus, only one set of programs was needed for both machines. A user can program both machines in a single language. Tests of the system with an application program indicate that is has very high potential. A major result of this work is the demonstration that a gigantic investment in new hardware is not necessary for computing facilities interested in graphics.« less

Reproducible Earth observation analytics: challenges, ideas, and a study case on containerized land use change detection

NASA Astrophysics Data System (ADS)

Appel, Marius; Nüst, Daniel; Pebesma, Edzer

2017-04-01

Geoscientific analyses of Earth observation data typically involve a long path from data acquisition to scientific results and conclusions. Before starting the actual processing, scenes must be downloaded from the providers' platforms and the computing infrastructure needs to be prepared. The computing environment often requires specialized software, which in turn might have lots of dependencies. The software is often highly customized and provided without commercial support, which leads to rather ad-hoc systems and irreproducible results. To let other scientists reproduce the analyses, the full workspace including data, code, the computing environment, and documentation must be bundled and shared. Technologies such as virtualization or containerization allow for the creation of identical computing environments with relatively little effort. Challenges, however, arise when the volume of the data is too large, when computations are done in a cluster environment, or when complex software components such as databases are used. We discuss these challenges for the example of scalable Land use change detection on Landsat imagery. We present a reproducible implementation that runs R and the scalable data management and analytical system SciDB within a Docker container. Thanks to an explicit container recipe (the Dockerfile), this enables the all-in-one reproduction including the installation of software components, the ingestion of the data, and the execution of the analysis in a well-defined environment. We furthermore discuss possibilities how the implementation could be transferred to multi-container environments in order to support reproducibility on large cluster environments.

Building quality into medical product software design.

PubMed

Mallory, S R

1993-01-01

The software engineering and quality assurance disciplines are a requisite to the design of safe and effective software-based medical devices. It is in the areas of software methodology and process that the most beneficial application of these disciplines to software development can be made. Software is a product of complex operations and methodologies and is not amenable to the traditional electromechanical quality assurance processes. Software quality must be built in by the developers, with the software verification and validation engineers acting as the independent instruments for ensuring compliance with performance objectives and with development and maintenance standards. The implementation of a software quality assurance program is a complex process involving management support, organizational changes, and new skill sets, but the benefits are profound. Its rewards provide safe, reliable, cost-effective, maintainable, and manageable software, which may significantly speed the regulatory review process and therefore potentially shorten the overall time to market. The use of a trial project can greatly facilitate the learning process associated with the first-time application of a software quality assurance program.

Alternatives to current flow cytometry data analysis for clinical and research studies.

PubMed

Gondhalekar, Carmen; Rajwa, Bartek; Patsekin, Valery; Ragheb, Kathy; Sturgis, Jennifer; Robinson, J Paul

2018-02-01

Flow cytometry has well-established methods for data analysis based on traditional data collection techniques. These techniques typically involved manual insertion of tube samples into an instrument that, historically, could only measure 1-3 colors. The field has since evolved to incorporate new technologies for faster and highly automated sample preparation and data collection. For example, the use of microwell plates on benchtop instruments is now a standard on virtually every new instrument, and so users can easily accumulate multiple data sets quickly. Further, because the user must carefully define the layout of the plate, this information is already defined when considering the analytical process, expanding the opportunities for automated analysis. Advances in multi-parametric data collection, as demonstrated by the development of hyperspectral flow-cytometry, 20-40 color polychromatic flow cytometry, and mass cytometry (CyTOF), are game-changing. As data and assay complexity increase, so too does the complexity of data analysis. Complex data analysis is already a challenge to traditional flow cytometry software. New methods for reviewing large and complex data sets can provide rapid insight into processes difficult to define without more advanced analytical tools. In settings such as clinical labs where rapid and accurate data analysis is a priority, rapid, efficient and intuitive software is needed. This paper outlines opportunities for analysis of complex data sets using examples of multiplexed bead-based assays, drug screens and cell cycle analysis - any of which could become integrated into the clinical environment. Copyright © 2017. Published by Elsevier Inc.

rpe v5: an emulator for reduced floating-point precision in large numerical simulations

NASA Astrophysics Data System (ADS)

Dawson, Andrew; Düben, Peter D.

2017-06-01

This paper describes the rpe (reduced-precision emulator) library which has the capability to emulate the use of arbitrary reduced floating-point precision within large numerical models written in Fortran. The rpe software allows model developers to test how reduced floating-point precision affects the result of their simulations without having to make extensive code changes or port the model onto specialized hardware. The software can be used to identify parts of a program that are problematic for numerical precision and to guide changes to the program to allow a stronger reduction in precision.The development of rpe was motivated by the strong demand for more computing power. If numerical precision can be reduced for an application under consideration while still achieving results of acceptable quality, computational cost can be reduced, since a reduction in numerical precision may allow an increase in performance or a reduction in power consumption. For simulations with weather and climate models, savings due to a reduction in precision could be reinvested to allow model simulations at higher spatial resolution or complexity, or to increase the number of ensemble members to improve predictions. rpe was developed with a particular focus on the community of weather and climate modelling, but the software could be used with numerical simulations from other domains.

Visualization for Molecular Dynamics Simulation of Gas and Metal Surface Interaction

NASA Astrophysics Data System (ADS)

Puzyrkov, D.; Polyakov, S.; Podryga, V.

2016-02-01

The development of methods, algorithms and applications for visualization of molecular dynamics simulation outputs is discussed. The visual analysis of the results of such calculations is a complex and actual problem especially in case of the large scale simulations. To solve this challenging task it is necessary to decide on: 1) what data parameters to render, 2) what type of visualization to choose, 3) what development tools to use. In the present work an attempt to answer these questions was made. For visualization it was offered to draw particles in the corresponding 3D coordinates and also their velocity vectors, trajectories and volume density in the form of isosurfaces or fog. We tested the way of post-processing and visualization based on the Python language with use of additional libraries. Also parallel software was developed that allows processing large volumes of data in the 3D regions of the examined system. This software gives the opportunity to achieve desired results that are obtained in parallel with the calculations, and at the end to collect discrete received frames into a video file. The software package "Enthought Mayavi2" was used as the tool for visualization. This visualization application gave us the opportunity to study the interaction of a gas with a metal surface and to closely observe the adsorption effect.

Software Process Assurance for Complex Electronics (SPACE)

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Complex Electronics (CE) are now programmed to perform tasks that were previously handled in software, such as communication protocols. Many of the methods used to develop software bare a close resemblance to CE development. For instance, Field Programmable Gate Arrays (FPGAs) can have over a million logic gates while system-on-chip (SOC) devices can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of software-like bugs such as incorrect design, logic, and unexpected interactions within the logic is great. Since CE devices are obscuring the hardware/software boundary, we propose that mature software methodologies may be utilized with slight modifications in the development of these devices. Software Process Assurance for Complex Electronics (SPACE) is a research project that looks at using standardized S/W Assurance/Engineering practices to provide an assurance framework for development activities. Tools such as checklists, best practices and techniques can be used to detect missing requirements and bugs earlier in the development cycle creating a development process for CE that will be more easily maintained, consistent and configurable based on the device used.

Integration of the instrument control electronics for the ESPRESSO spectrograph at ESO-VLT

NASA Astrophysics Data System (ADS)

Baldini, V.; Calderone, G.; Cirami, R.; Coretti, I.; Cristiani, S.; Di Marcantonio, P.; Mégevand, D.; Riva, M.; Santin, P.

2016-07-01

ESPRESSO, the Echelle SPectrograph for Rocky Exoplanet and Stable Spectroscopic Observations of the ESO - Very Large Telescope site, is now in its integration phase. The large number of functions of this complex instrument are fully controlled by a Beckhoff PLC based control electronics architecture. Four small and one large cabinets host the main electronic parts to control all the sensors, motorized stages and other analogue and digital functions of ESPRESSO. The Instrument Control Electronics (ICE) is built following the latest ESO standards and requirements. Two main PLC CPUs are used and are programmed through the TwinCAT Beckhoff dedicated software. The assembly, integration and verification phase of ESPRESSO, due to its distributed nature and different geographical locations of the consortium partners, is quite challenging. After the preliminary assembling and test of the electronic components at the Astronomical Observatory of Trieste and the test of some electronics and software parts at ESO (Garching), the complete system for the control of the four Front End Unit (FEU) arms of ESPRESSO has been fully assembled and tested in Merate (Italy) at the beginning of 2016. After these first tests, the system will be located at the Geneva Observatory (Switzerland) until the Preliminary Acceptance Europe (PAE) and finally shipped to Chile for the commissioning. This paper describes the integration strategy of the ICE workpackage of ESPRESSO, the hardware and software tests that have been performed, with an overall view of the experience gained during these project's phases.

Probabilistic structural mechanics research for parallel processing computers

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Chen, Heh-Chyun; Twisdale, Lawrence A.; Martin, William R.

1991-01-01

Aerospace structures and spacecraft are a complex assemblage of structural components that are subjected to a variety of complex, cyclic, and transient loading conditions. Significant modeling uncertainties are present in these structures, in addition to the inherent randomness of material properties and loads. To properly account for these uncertainties in evaluating and assessing the reliability of these components and structures, probabilistic structural mechanics (PSM) procedures must be used. Much research has focused on basic theory development and the development of approximate analytic solution methods in random vibrations and structural reliability. Practical application of PSM methods was hampered by their computationally intense nature. Solution of PSM problems requires repeated analyses of structures that are often large, and exhibit nonlinear and/or dynamic response behavior. These methods are all inherently parallel and ideally suited to implementation on parallel processing computers. New hardware architectures and innovative control software and solution methodologies are needed to make solution of large scale PSM problems practical.

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging.

PubMed

Held, Michael; Schmitz, Michael H A; Fischer, Bernd; Walter, Thomas; Neumann, Beate; Olma, Michael H; Peter, Matthias; Ellenberg, Jan; Gerlich, Daniel W

2010-09-01

Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. Incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions and confusion between different functional states with similar morphology. We demonstrate generic applicability in different assays and perturbation conditions, including a candidate-based RNA interference screen for regulators of mitotic exit in human cells. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.

New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content

PubMed Central

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT. PMID:23304293

New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content.

PubMed

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT.

Software system safety

NASA Technical Reports Server (NTRS)

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.

TriBITS lifecycle model. Version 1.0, a lean/agile software lifecycle model for research-based computational science and engineering and applied mathematical software.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willenbring, James M.; Bartlett, Roscoe Ainsworth; Heroux, Michael Allen

2012-01-01

Software lifecycles are becoming an increasingly important issue for computational science and engineering (CSE) software. The process by which a piece of CSE software begins life as a set of research requirements and then matures into a trusted high-quality capability is both commonplace and extremely challenging. Although an implicit lifecycle is obviously being used in any effort, the challenges of this process - respecting the competing needs of research vs. production - cannot be overstated. Here we describe a proposal for a well-defined software lifecycle process based on modern Lean/Agile software engineering principles. What we propose is appropriate for manymore » CSE software projects that are initially heavily focused on research but also are expected to eventually produce usable high-quality capabilities. The model is related to TriBITS, a build, integration and testing system, which serves as a strong foundation for this lifecycle model, and aspects of this lifecycle model are ingrained in the TriBITS system. Here, we advocate three to four phases or maturity levels that address the appropriate handling of many issues associated with the transition from research to production software. The goals of this lifecycle model are to better communicate maturity levels with customers and to help to identify and promote Software Engineering (SE) practices that will help to improve productivity and produce better software. An important collection of software in this domain is Trilinos, which is used as the motivation and the initial target for this lifecycle model. However, many other related and similar CSE (and non-CSE) software projects can also make good use of this lifecycle model, especially those that use the TriBITS system. Indeed this lifecycle process, if followed, will enable large-scale sustainable integration of many complex CSE software efforts across several institutions.« less

Massive Multi-Agent Systems Control

NASA Technical Reports Server (NTRS)

Campagne, Jean-Charles; Gardon, Alain; Collomb, Etienne; Nishida, Toyoaki

2004-01-01

In order to build massive multi-agent systems, considered as complex and dynamic systems, one needs a method to analyze and control the system. We suggest an approach using morphology to represent and control the state of large organizations composed of a great number of light software agents. Morphology is understood as representing the state of the multi-agent system as shapes in an abstract geometrical space, this notion is close to the notion of phase space in physics.

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

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

2014-01-01

Motivation: 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. Results: 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. Availability and implementation: 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. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Using Java for distributed computing in the Gaia satellite data processing

NASA Astrophysics Data System (ADS)

O'Mullane, William; Luri, Xavier; Parsons, Paul; Lammers, Uwe; Hoar, John; Hernandez, Jose

2011-10-01

In recent years Java has matured to a stable easy-to-use language with the flexibility of an interpreter (for reflection etc.) but the performance and type checking of a compiled language. When we started using Java for astronomical applications around 1999 they were the first of their kind in astronomy. Now a great deal of astronomy software is written in Java as are many business applications. We discuss the current environment and trends concerning the language and present an actual example of scientific use of Java for high-performance distributed computing: ESA's mission Gaia. The Gaia scanning satellite will perform a galactic census of about 1,000 million objects in our galaxy. The Gaia community has chosen to write its processing software in Java. We explore the manifold reasons for choosing Java for this large science collaboration. Gaia processing is numerically complex but highly distributable, some parts being embarrassingly parallel. We describe the Gaia processing architecture and its realisation in Java. We delve into the astrometric solution which is the most advanced and most complex part of the processing. The Gaia simulator is also written in Java and is the most mature code in the system. This has been successfully running since about 2005 on the supercomputer "Marenostrum" in Barcelona. We relate experiences of using Java on a large shared machine. Finally we discuss Java, including some of its problems, for scientific computing.

Particle physics and polyedra proximity calculation for hazard simulations in large-scale industrial plants

NASA Astrophysics Data System (ADS)

Plebe, Alice; Grasso, Giorgio

2016-12-01

This paper describes a system developed for the simulation of flames inside an open-source 3D computer graphic software, Blender, with the aim of analyzing in virtual reality scenarios of hazards in large-scale industrial plants. The advantages of Blender are of rendering at high resolution the very complex structure of large industrial plants, and of embedding a physical engine based on smoothed particle hydrodynamics. This particle system is used to evolve a simulated fire. The interaction of this fire with the components of the plant is computed using polyhedron separation distance, adopting a Voronoi-based strategy that optimizes the number of feature distance computations. Results on a real oil and gas refining industry are presented.

Pitch sensation involves stochastic resonance

PubMed Central

Martignoli, Stefan; Gomez, Florian; Stoop, Ruedi

2013-01-01

Pitch is a complex hearing phenomenon that results from elicited and self-generated cochlear vibrations. Read-off vibrational information is relayed higher up the auditory pathway, where it is then condensed into pitch sensation. How this can adequately be described in terms of physics has largely remained an open question. We have developed a peripheral hearing system (in hardware and software) that reproduces with great accuracy all salient pitch features known from biophysical and psychoacoustic experiments. At the level of the auditory nerve, the system exploits stochastic resonance to achieve this performance, which may explain the large amount of noise observed in the working auditory nerve. PMID:24045830

Managing large-scale workflow execution from resource provisioning to provenance tracking: The CyberShake example

USGS Publications Warehouse

Deelman, E.; Callaghan, S.; Field, E.; Francoeur, H.; Graves, R.; Gupta, N.; Gupta, V.; Jordan, T.H.; Kesselman, C.; Maechling, P.; Mehringer, J.; Mehta, G.; Okaya, D.; Vahi, K.; Zhao, L.

2006-01-01

This paper discusses the process of building an environment where large-scale, complex, scientific analysis can be scheduled onto a heterogeneous collection of computational and storage resources. The example application is the Southern California Earthquake Center (SCEC) CyberShake project, an analysis designed to compute probabilistic seismic hazard curves for sites in the Los Angeles area. We explain which software tools were used to build to the system, describe their functionality and interactions. We show the results of running the CyberShake analysis that included over 250,000 jobs using resources available through SCEC and the TeraGrid. ?? 2006 IEEE.

Sonification Prototype for Space Physics

NASA Astrophysics Data System (ADS)

Candey, R. M.; Schertenleib, A. M.; Diaz Merced, W. L.

2005-12-01

As an alternative and adjunct to visual displays, auditory exploration of data via sonification (data controlled sound) and audification (audible playback of data samples) is promising for complex or rapidly/temporally changing visualizations, for data exploration of large datasets (particularly multi-dimensional datasets), and for exploring datasets in frequency rather than spatial dimensions (see also International Conferences on Auditory Display ). Besides improving data exploration and analysis for most researchers, the use of sound is especially valuable as an assistive technology for visually-impaired people and can make science and math more exciting for high school and college students. Only recently have the hardware and software come together to make a cross-platform open-source sonification tool feasible. We have developed a prototype sonification data analysis tool using the JavaSound API and NASA GSFC's ViSBARD software . Wanda Diaz Merced, a blind astrophysicist from Puerto Rico, is instrumental in advising on and testing the tool.

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Software for project-based learning of robot motion planning

NASA Astrophysics Data System (ADS)

Moll, Mark; Bordeaux, Janice; Kavraki, Lydia E.

2013-12-01

Motion planning is a core problem in robotics concerned with finding feasible paths for a given robot. Motion planning algorithms perform a search in the high-dimensional continuous space of robot configurations and exemplify many of the core algorithmic concepts of search algorithms and associated data structures. Motion planning algorithms can be explained in a simplified two-dimensional setting, but this masks many of the subtleties and complexities of the underlying problem. We have developed software for project-based learning of motion planning that enables deep learning. The projects that we have developed allow advanced undergraduate students and graduate students to reflect on the performance of existing textbook algorithms and their own variations on such algorithms. Formative assessment has been conducted at three institutions. The core of the software used for this teaching module is also used within the Robot Operating System, a widely adopted platform by the robotics research community. This allows for transfer of knowledge and skills to robotics research projects involving a large variety robot hardware platforms.

Service-oriented architecture for the ARGOS instrument control software

NASA Astrophysics Data System (ADS)

Borelli, J.; Barl, L.; Gässler, W.; Kulas, M.; Rabien, Sebastian

2012-09-01

The Advanced Rayleigh Guided ground layer Adaptive optic System, ARGOS, equips the Large Binocular Telescope (LBT) with a constellation of six rayleigh laser guide stars. By correcting atmospheric turbulence near the ground, the system is designed to increase the image quality of the multi-object spectrograph LUCIFER approximately by a factor of 3 over a field of 4 arc minute diameter. The control software has the critical task of orchestrating several devices, instruments, and high level services, including the already existing adaptive optic system and the telescope control software. All these components are widely distributed over the telescope, adding more complexity to the system design. The approach used by the ARGOS engineers is to write loosely coupled and distributed services under the control of different ownership systems, providing a uniform mechanism to offer, discover, interact and use these distributed capabilities. The control system counts with several finite state machines, vibration and flexure compensation loops, and safety mechanism, such as interlocks, aircraft, and satellite avoidance systems.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

PubMed

Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

2003-11-01

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

PubMed

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

Scalability and Validation of Big Data Bioinformatics Software.

PubMed

Yang, Andrian; Troup, Michael; Ho, Joshua W K

2017-01-01

This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs. Nonetheless the surge of volume and variety of biological and biomedical data has posed new challenges. We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment. Validation of software is another important issue in big data bioinformatics that is often ignored. Software validation is the process of determining whether the program under test fulfils the task for which it was designed. Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved. We discuss how state-of-the-art software testing techniques that are based on the idea of multiple executions, such as metamorphic testing, can be used to implement an effective bioinformatics quality assurance strategy. We hope this review will raise awareness of these critical issues in bioinformatics.

Validating the simulation of large-scale parallel applications using statistical characteristics

DOE PAGES

Zhang, Deli; Wilke, Jeremiah; Hendry, Gilbert; ...

2016-03-01

Simulation is a widely adopted method to analyze and predict the performance of large-scale parallel applications. Validating the hardware model is highly important for complex simulations with a large number of parameters. Common practice involves calculating the percent error between the projected and the real execution time of a benchmark program. However, in a high-dimensional parameter space, this coarse-grained approach often suffers from parameter insensitivity, which may not be known a priori. Moreover, the traditional approach cannot be applied to the validation of software models, such as application skeletons used in online simulations. In this work, we present a methodologymore » and a toolset for validating both hardware and software models by quantitatively comparing fine-grained statistical characteristics obtained from execution traces. Although statistical information has been used in tasks like performance optimization, this is the first attempt to apply it to simulation validation. Lastly, our experimental results show that the proposed evaluation approach offers significant improvement in fidelity when compared to evaluation using total execution time, and the proposed metrics serve as reliable criteria that progress toward automating the simulation tuning process.« less

Software Accelerates Computing Time for Complex Math

NASA Technical Reports Server (NTRS)

2014-01-01

Ames Research Center awarded Newark, Delaware-based EM Photonics Inc. SBIR funding to utilize graphic processing unit (GPU) technology- traditionally used for computer video games-to develop high-computing software called CULA. The software gives users the ability to run complex algorithms on personal computers with greater speed. As a result of the NASA collaboration, the number of employees at the company has increased 10 percent.

Software-engineering challenges of building and deploying reusable problem solvers.

PubMed

O'Connor, Martin J; Nyulas, Csongor; Tu, Samson; Buckeridge, David L; Okhmatovskaia, Anna; Musen, Mark A

2009-11-01

Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ultimate objective is to produce libraries of methods that can be easily adapted for use in these systems. Despite the intuitive appeal of PSMs as conceptual building blocks, in practice, these goals are largely unmet. There are no widely available tools for building applications using PSMs and no public libraries of PSMs available for reuse. This paper analyzes some of the reasons for the lack of widespread adoptions of PSM techniques and illustrate our analysis by describing our experiences developing a complex, high-throughput software system based on PSM principles. We conclude that many fundamental principles in PSM research are useful for building knowledge-based systems. In particular, the task-method decomposition process, which provides a means for structuring knowledge-based tasks, is a powerful abstraction for building systems of analytic methods. However, despite the power of PSMs in the conceptual modeling of knowledge-based systems, software engineering challenges have been seriously underestimated. The complexity of integrating control knowledge modeled by developers using PSMs with the domain knowledge that they model using ontologies creates a barrier to widespread use of PSM-based systems. Nevertheless, the surge of recent interest in ontologies has led to the production of comprehensive domain ontologies and of robust ontology-authoring tools. These developments present new opportunities to leverage the PSM approach.

Software-engineering challenges of building and deploying reusable problem solvers

PubMed Central

O’CONNOR, MARTIN J.; NYULAS, CSONGOR; TU, SAMSON; BUCKERIDGE, DAVID L.; OKHMATOVSKAIA, ANNA; MUSEN, MARK A.

2012-01-01

Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ultimate objective is to produce libraries of methods that can be easily adapted for use in these systems. Despite the intuitive appeal of PSMs as conceptual building blocks, in practice, these goals are largely unmet. There are no widely available tools for building applications using PSMs and no public libraries of PSMs available for reuse. This paper analyzes some of the reasons for the lack of widespread adoptions of PSM techniques and illustrate our analysis by describing our experiences developing a complex, high-throughput software system based on PSM principles. We conclude that many fundamental principles in PSM research are useful for building knowledge-based systems. In particular, the task–method decomposition process, which provides a means for structuring knowledge-based tasks, is a powerful abstraction for building systems of analytic methods. However, despite the power of PSMs in the conceptual modeling of knowledge-based systems, software engineering challenges have been seriously underestimated. The complexity of integrating control knowledge modeled by developers using PSMs with the domain knowledge that they model using ontologies creates a barrier to widespread use of PSM-based systems. Nevertheless, the surge of recent interest in ontologies has led to the production of comprehensive domain ontologies and of robust ontology-authoring tools. These developments present new opportunities to leverage the PSM approach. PMID:23565031

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

Attributes and Behaviors of Performance-Centered Systems.

ERIC Educational Resources Information Center

Gery, Gloria

1995-01-01

Examines attributes, characteristics, and behaviors of performance-centered software packages that are emerging in the consumer software marketplace and compares them with large-scale systems software being designed by internal information systems staffs and vendors of large-scale software designed for financial, manufacturing, processing, and…

The application of dynamic programming in production planning

NASA Astrophysics Data System (ADS)

Wu, Run

2017-05-01

Nowadays, with the popularity of the computers, various industries and fields are widely applying computer information technology, which brings about huge demand for a variety of application software. In order to develop software meeting various needs with most economical cost and best quality, programmers must design efficient algorithms. A superior algorithm can not only soul up one thing, but also maximize the benefits and generate the smallest overhead. As one of the common algorithms, dynamic programming algorithms are used to solving problems with some sort of optimal properties. When solving problems with a large amount of sub-problems that needs repetitive calculations, the ordinary sub-recursive method requires to consume exponential time, and dynamic programming algorithm can reduce the time complexity of the algorithm to the polynomial level, according to which we can conclude that dynamic programming algorithm is a very efficient compared to other algorithms reducing the computational complexity and enriching the computational results. In this paper, we expound the concept, basic elements, properties, core, solving steps and difficulties of the dynamic programming algorithm besides, establish the dynamic programming model of the production planning problem.

Gray: a ray tracing-based Monte Carlo simulator for PET

NASA Astrophysics Data System (ADS)

Freese, David L.; Olcott, Peter D.; Buss, Samuel R.; Levin, Craig S.

2018-05-01

Monte Carlo simulation software plays a critical role in PET system design. Performing complex, repeated Monte Carlo simulations can be computationally prohibitive, as even a single simulation can require a large amount of time and a computing cluster to complete. Here we introduce Gray, a Monte Carlo simulation software for PET systems. Gray exploits ray tracing methods used in the computer graphics community to greatly accelerate simulations of PET systems with complex geometries. We demonstrate the implementation of models for positron range, annihilation acolinearity, photoelectric absorption, Compton scatter, and Rayleigh scatter. For validation, we simulate the GATE PET benchmark, and compare energy, distribution of hits, coincidences, and run time. We show a speedup using Gray, compared to GATE for the same simulation, while demonstrating nearly identical results. We additionally simulate the Siemens Biograph mCT system with both the NEMA NU-2 scatter phantom and sensitivity phantom. We estimate the total sensitivity within % when accounting for differences in peak NECR. We also estimate the peak NECR to be kcps, or within % of published experimental data. The activity concentration of the peak is also estimated within 1.3%.

Efficient computation of the joint sample frequency spectra for multiple populations.

PubMed

Kamm, John A; Terhorst, Jonathan; Song, Yun S

2017-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity.

Efficient computation of the joint sample frequency spectra for multiple populations

PubMed Central

Kamm, John A.; Terhorst, Jonathan; Song, Yun S.

2016-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity. PMID:28239248

scraps: An open-source Python-based analysis package for analyzing and plotting superconducting resonator data

DOE PAGES

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn; ...

2016-11-07

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

Data management integration for biomedical core facilities

NASA Astrophysics Data System (ADS)

Zhang, Guo-Qiang; Szymanski, Jacek; Wilson, David

2007-03-01

We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

Spacecraft Avionics Software Development Then and Now: Different but the Same

NASA Technical Reports Server (NTRS)

Mangieri, Mark L.; Garman, John (Jack); Vice, Jason

2012-01-01

NASA has always been in the business of balancing new technologies and techniques to achieve human space travel objectives. NASA s historic Software Production Facility (SPF) was developed to serve complex avionics software solutions during an era dominated by mainframes, tape drives, and lower level programming languages. These systems have proven themselves resilient enough to serve the Shuttle Orbiter Avionics life cycle for decades. The SPF and its predecessor the Software Development Lab (SDL) at NASA s Johnson Space Center (JSC) hosted flight software (FSW) engineering, development, simulation, and test. It was active from the beginning of Shuttle Orbiter development in 1972 through the end of the shuttle program in the summer of 2011 almost 40 years. NASA s Kedalion engineering analysis lab is on the forefront of validating and using many contemporary avionics HW/SW development and integration techniques, which represent new paradigms to NASA s heritage culture in avionics software engineering. Kedalion has validated many of the Orion project s HW/SW engineering techniques borrowed from the adjacent commercial aircraft avionics environment, inserting new techniques and skills into the Multi-Purpose Crew Vehicle (MPCV) Orion program. Using contemporary agile techniques, COTS products, early rapid prototyping, in-house expertise and tools, and customer collaboration, NASA has adopted a cost effective paradigm that is currently serving Orion effectively. This paper will explore and contrast differences in technology employed over the years of NASA s space program, due largely to technological advances in hardware and software systems, while acknowledging that the basic software engineering and integration paradigms share many similarities.

Managing Complexity in Next Generation Robotic Spacecraft: From a Software Perspective

NASA Technical Reports Server (NTRS)

Reinholtz, Kirk

2008-01-01

This presentation highlights the challenges in the design of software to support robotic spacecraft. Robotic spacecraft offer a higher degree of autonomy, however currently more capabilities are required, primarily in the software, while providing the same or higher degree of reliability. The complexity of designing such an autonomous system is great, particularly while attempting to address the needs for increased capabilities and high reliability without increased needs for time or money. The efforts to develop programming models for the new hardware and the integration of software architecture are highlighted.

RevEcoR: an R package for the reverse ecology analysis of microbiomes.

PubMed

Cao, Yang; Wang, Yuanyuan; Zheng, Xiaofei; Li, Fei; Bo, Xiaochen

2016-07-29

All species live in complex ecosystems. The structure and complexity of a microbial community reflects not only diversity and function, but also the environment in which it occurs. However, traditional ecological methods can only be applied on a small scale and for relatively well-understood biological systems. Recently, a graph-theory-based algorithm called the reverse ecology approach has been developed that can analyze the metabolic networks of all the species in a microbial community, and predict the metabolic interface between species and their environment. Here, we present RevEcoR, an R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities. This software allows users to obtain large-scale ecological insights into species' ecology directly from high-throughput metagenomic data. The software has great potential for facilitating the study of microbiomes. RevEcoR is open source software for the study of microbial community ecology. The RevEcoR R package is freely available under the GNU General Public License v. 2.0 at http://cran.r-project.org/web/packages/RevEcoR/ with the vignette and typical usage examples, and the interactive Shiny web application is available at http://yiluheihei.shinyapps.io/shiny-RevEcoR , or can be installed locally with the source code accessed from https://github.com/yiluheihei/shiny-RevEcoR .

Next-Generation Lightweight Mirror Modeling Software

NASA Technical Reports Server (NTRS)

Arnold, William R., Sr.; Fitzgerald, Mathew; Rosa, Rubin Jaca; Stahl, Phil

2013-01-01

The advances in manufacturing techniques for lightweight mirrors, such as EXELSIS deep core low temperature fusion, Corning's continued improvements in the Frit bonding process and the ability to cast large complex designs, combined with water-jet and conventional diamond machining of glasses and ceramics has created the need for more efficient means of generating finite element models of these structures. Traditional methods of assembling 400,000 + element models can take weeks of effort, severely limiting the range of possible optimization variables. This paper will introduce model generation software developed under NASA sponsorship for the design of both terrestrial and space based mirrors. The software deals with any current mirror manufacturing technique, single substrates, multiple arrays of substrates, as well as the ability to merge submodels into a single large model. The modeler generates both mirror and suspension system elements, suspensions can be created either for each individual petal or the whole mirror. A typical model generation of 250,000 nodes and 450,000 elements only takes 5-10 minutes, much of that time being variable input time. The program can create input decks for ANSYS, ABAQUS and NASTRAN. An archive/retrieval system permits creation of complete trade studies, varying cell size, depth, and petal size, suspension geometry with the ability to recall a particular set of parameters and make small or large changes with ease. The input decks created by the modeler are text files which can be modified by any editor, all the key shell thickness parameters are accessible and comments in deck identify which groups of elements are associated with these parameters. This again makes optimization easier. With ANSYS decks, the nodes representing support attachments are grouped into components; in ABAQUS these are SETS and in NASTRAN as GRIDPOINT SETS, this make integration of these models into large telescope or satellite models possible

Next Generation Lightweight Mirror Modeling Software

NASA Technical Reports Server (NTRS)

Arnold, William; Fitzgerald, Matthew; Stahl, Philip

2013-01-01

The advances in manufacturing techniques for lightweight mirrors, such as EXELSIS deep core low temperature fusion, Corning's continued improvements in the Frit bonding process and the ability to cast large complex designs, combined with water-jet and conventional diamond machining of glasses and ceramics has created the need for more efficient means of generating finite element models of these structures. Traditional methods of assembling 400,000 + element models can take weeks of effort, severely limiting the range of possible optimization variables. This paper will introduce model generation software developed under NASA sponsorship for the design of both terrestrial and space based mirrors. The software deals with any current mirror manufacturing technique, single substrates, multiple arrays of substrates, as well as the ability to merge submodels into a single large model. The modeler generates both mirror and suspension system elements, suspensions can be created either for each individual petal or the whole mirror. A typical model generation of 250,000 nodes and 450,000 elements only takes 5-10 minutes, much of that time being variable input time. The program can create input decks for ANSYS, ABAQUS and NASTRAN. An archive/retrieval system permits creation of complete trade studies, varying cell size, depth, and petal size, suspension geometry with the ability to recall a particular set of parameters and make small or large changes with ease. The input decks created by the modeler are text files which can be modified by any editor, all the key shell thickness parameters are accessible and comments in deck identify which groups of elements are associated with these parameters. This again makes optimization easier. With ANSYS decks, the nodes representing support attachments are grouped into components; in ABAQUS these are SETS and in NASTRAN as GRIDPOINT SETS, this make integration of these models into large telescope or satellite models possible.

Next Generation Lightweight Mirror Modeling Software

NASA Technical Reports Server (NTRS)

Arnold, William R., Sr.; Fitzgerald, Mathew; Rosa, Rubin Jaca; Stahl, H. Philip

2013-01-01

The advances in manufacturing techniques for lightweight mirrors, such as EXELSIS deep core low temperature fusion, Corning's continued improvements in the Frit bonding process and the ability to cast large complex designs, combined with water-jet and conventional diamond machining of glasses and ceramics has created the need for more efficient means of generating finite element models of these structures. Traditional methods of assembling 400,000 + element models can take weeks of effort, severely limiting the range of possible optimization variables. This paper will introduce model generation software developed under NASA sponsorship for the design of both terrestrial and space based mirrors. The software deals with any current mirror manufacturing technique, single substrates, multiple arrays of substrates, as well as the ability to merge submodels into a single large model. The modeler generates both mirror and suspension system elements, suspensions can be created either for each individual petal or the whole mirror. A typical model generation of 250,000 nodes and 450,000 elements only takes 5-10 minutes, much of that time being variable input time. The program can create input decks for ANSYS, ABAQUS and NASTRAN. An archive/retrieval system permits creation of complete trade studies, varying cell size, depth, and petal size, suspension geometry with the ability to recall a particular set of parameters and make small or large changes with ease. The input decks created by the modeler are text files which can be modified by any editor, all the key shell thickness parameters are accessible and comments in deck identify which groups of elements are associated with these parameters. This again makes optimization easier. With ANSYS decks, the nodes representing support attachments are grouped into components; in ABAQUS these are SETS and in NASTRAN as GRIDPOINT SETS, this make integration of these models into large telescope or satellite models easier.

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos.

PubMed

Giurumescu, Claudiu A; Kang, Sukryool; Planchon, Thomas A; Betzig, Eric; Bloomekatz, Joshua; Yelon, Deborah; Cosman, Pamela; Chisholm, Andrew D

2012-11-01

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking.

Integrating Testing into Software Engineering Courses Supported by a Collaborative Learning Environment

ERIC Educational Resources Information Center

Clarke, Peter J.; Davis, Debra; King, Tariq M.; Pava, Jairo; Jones, Edward L.

2014-01-01

As software becomes more ubiquitous and complex, the cost of software bugs continues to grow at a staggering rate. To remedy this situation, there needs to be major improvement in the knowledge and application of software validation techniques. Although there are several software validation techniques, software testing continues to be one of the…

Better software, better research: the challenge of preserving your research and your reputation

NASA Astrophysics Data System (ADS)

Chue Hong, N.

2017-12-01

Software is fundamental to research. From short, thrown-together temporary scripts, through an abundance of complex spreadsheets analysing collected data, to the hundreds of software engineers and millions of lines of code behind international efforts such as the Large Hadron Collider and the Square Kilometre Array, software has made an invaluable contribution to advancing our research knowledge. Within the earth and space sciences, data is being generated, collected, processed and analysed in ever greater amounts and detail. However the pace of this improvement leads to challenges around the persistence of research outputs and artefacts. A specific challenge in this field is that often experiments and measurements cannot be repeated, yet the infrastructure used to manage, store and process this data must be continually updated and developed: constant change just to stay still. The UK-based Software Sustainability Institute (SSI) aims to improve research software sustainability, working with researchers, funders, research software engineers, managers, and other stakeholders across the research spectrum. In this talk, I will present lessons learned and good practice based on the work of the Institute and its collaborators. I will summarise some of the work that is being done to improve the integration of infrastructure for managing research outputs, including around software citation and reward, extending data management plans, and improving researcher skills: "better software, better research". Ultimately, being a modern researcher in the geosciences requires you to efficiently balance the pursuit of new knowledge with making your work reusable and reproducible. And as scientists are placed under greater scrutiny about whether others can trust their results, the preservation of your artefacts has a key role in the preservation of your reputation.

Software and hardware complex for research and management of the separation process

NASA Astrophysics Data System (ADS)

Borisov, A. P.

2018-01-01

The article is devoted to the development of a program for studying the operation of an asynchronous electric drive using vector-algorithmic switching of windings, as well as the development of a hardware-software complex for controlling parameters and controlling the speed of rotation of an asynchronous electric drive for investigating the operation of a cyclone. To study the operation of an asynchronous electric drive, a method was used in which the average value of flux linkage is found and a method for vector-algorithmic calculation of the power and electromagnetic moment of an asynchronous electric drive feeding from a single-phase network is developed, with vector-algorithmic commutation, and software for calculating parameters. The software part of the complex allows to regulate the speed of rotation of the motor by vector-algorithmic switching of transistors or, using pulse-width modulation (PWM), set any engine speed. Also sensors are connected to the hardware-software complex at the inlet and outlet of the cyclone. The developed cyclone with an inserted complex allows to receive high efficiency of product separation at various entrance speeds. At an inlet air speed of 18 m / s, the cyclone’s maximum efficiency is achieved. For this, it is necessary to provide the rotational speed of an asynchronous electric drive with a frequency of 45 Hz.

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications.

PubMed

Pascal, Bruce D; West, Graham M; Scharager-Tapia, Catherina; Flefil, Ricardo; Moroni, Tina; Martinez-Acedo, Pablo; Griffin, Patrick R; Carvalloza, Anthony C

2015-12-01

The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS(1) data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS(1) data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS(2) analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com . Graphical Abstract ᅟ.

Health care professional workstation: software system construction using DSSA scenario-based engineering process.

PubMed

Hufnagel, S; Harbison, K; Silva, J; Mettala, E

1994-01-01

This paper describes a new method for the evolutionary determination of user requirements and system specifications called scenario-based engineering process (SEP). Health care professional workstations are critical components of large scale health care system architectures. We suggest that domain-specific software architectures (DSSAs) be used to specify standard interfaces and protocols for reusable software components throughout those architectures, including workstations. We encourage the use of engineering principles and abstraction mechanisms. Engineering principles are flexible guidelines, adaptable to particular situations. Abstraction mechanisms are simplifications for management of complexity. We recommend object-oriented design principles, graphical structural specifications, and formal components' behavioral specifications. We give an ambulatory care scenario and associated models to demonstrate SEP. The scenario uses health care terminology and gives patients' and health care providers' system views. Our goal is to have a threefold benefit. (i) Scenario view abstractions provide consistent interdisciplinary communications. (ii) Hierarchical object-oriented structures provide useful abstractions for reuse, understandability, and long term evolution. (iii) SEP and health care DSSA integration into computer aided software engineering (CASE) environments. These environments should support rapid construction and certification of individualized systems, from reuse libraries.

Integration of an expert system into a user interface language demonstration

NASA Technical Reports Server (NTRS)

Stclair, D. C.

1986-01-01

The need for a User Interface Language (UIL) has been recognized by the Space Station Program Office as a necessary tool to aid in minimizing the cost of software generation by multiple users. Previous history in the Space Shuttle Program has shown that many different areas of software generation, such as operations, integration, testing, etc., have each used a different user command language although the types of operations being performed were similar in many respects. Since the Space Station represents a much more complex software task, a common user command language--a user interface language--is required to support the large spectrum of space station software developers and users. To assist in the selection of an appropriate set of definitions for a UIL, a series of demonstration programs was generated with which to test UIL concepts against specific Space Station scenarios using operators for the astronaut and scientific community. Because of the importance of expert system in the space station, it was decided that an expert system should be embedded in the UIL. This would not only provide insight into the UIL components required but would indicate the effectiveness with which an expert system could function in such an environment.

Design and implementation of software for automated quality control and data analysis for a complex LC/MS/MS assay for urine opiates and metabolites.

PubMed

Dickerson, Jane A; Schmeling, Michael; Hoofnagle, Andrew N; Hoffman, Noah G

2013-01-16

Mass spectrometry provides a powerful platform for performing quantitative, multiplexed assays in the clinical laboratory, but at the cost of increased complexity of analysis and quality assurance calculations compared to other methodologies. Here we describe the design and implementation of a software application that performs quality control calculations for a complex, multiplexed, mass spectrometric analysis of opioids and opioid metabolites. The development and implementation of this application improved our data analysis and quality assurance processes in several ways. First, use of the software significantly improved the procedural consistency for performing quality control calculations. Second, it reduced the amount of time technologists spent preparing and reviewing the data, saving on average over four hours per run, and in some cases improving turnaround time by a day. Third, it provides a mechanism for coupling procedural and software changes with the results of each analysis. We describe several key details of the implementation including the use of version control software and automated unit tests. These generally useful software engineering principles should be considered for any software development project in the clinical lab. Copyright © 2012 Elsevier B.V. All rights reserved.

Large-scale structural analysis: The structural analyst, the CSM Testbed and the NAS System

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Mccleary, Susan L.; Macy, Steven C.; Aminpour, Mohammad A.

1989-01-01

The Computational Structural Mechanics (CSM) activity is developing advanced structural analysis and computational methods that exploit high-performance computers. Methods are developed in the framework of the CSM testbed software system and applied to representative complex structural analysis problems from the aerospace industry. An overview of the CSM testbed methods development environment is presented and some numerical methods developed on a CRAY-2 are described. Selected application studies performed on the NAS CRAY-2 are also summarized.

Advanced Artificial Intelligence Technology Testbed

NASA Technical Reports Server (NTRS)

Anken, Craig S.

1993-01-01

The Advanced Artificial Intelligence Technology Testbed (AAITT) is a laboratory testbed for the design, analysis, integration, evaluation, and exercising of large-scale, complex, software systems, composed of both knowledge-based and conventional components. The AAITT assists its users in the following ways: configuring various problem-solving application suites; observing and measuring the behavior of these applications and the interactions between their constituent modules; gathering and analyzing statistics about the occurrence of key events; and flexibly and quickly altering the interaction of modules within the applications for further study.

Documentation Driven Development for Complex Real-Time Systems

DTIC Science & Technology

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

Coordinating the Complexity of Tools, Tasks, and Users: On Theory-Based Approaches to Authoring Tool Usability

ERIC Educational Resources Information Center

Murray, Tom

2016-01-01

Intelligent Tutoring Systems authoring tools are highly complex educational software applications used to produce highly complex software applications (i.e. ITSs). How should our assumptions about the target users (authors) impact the design of authoring tools? In this article I first reflect on the factors leading to my original 1999 article on…

Proceedings of the Ninth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1984-01-01

Experiences in measurement, utilization, and evaluation of software methodologies, models, and tools are discussed. NASA's involvement in ever larger and more complex systems, like the space station project, provides a motive for the support of software engineering research and the exchange of ideas in such forums. The topics of current SEL research are software error studies, experiments with software development, and software tools.

Submarine pipeline on-bottom stability. Volume 2: Software and manuals

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-12-01

The state-of-the-art in pipeline stability design has been changing very rapidly recent. The physics governing on-bottom stability are much better understood now than they were eight years. This is due largely because of research and large scale model tests sponsored by PRCI. Analysis tools utilizing this new knowledge have been developed. These tools provide the design engineer with a rational approach have been developed. These tools provide the design engineer with a rational approach for weight coating design, which he can use with confidence because the tools have been developed based on full scale and near full scale model tests.more » These tools represent the state-of-the-art in stability design and model the complex behavior of pipes subjected to both wave and current loads. These include: hydrodynamic forces which account for the effect of the wake (generated by flow over the pipe) washing back and forth over the pipe in oscillatory flow; and the embedment (digging) which occurs as a pipe resting on the seabed is exposed to oscillatory loadings and small oscillatory deflections. This report has been developed as a reference handbook for use in on-bottom pipeline stability analysis It consists of two volumes. Volume one is devoted descriptions of the various aspects of the problem: the pipeline design process; ocean physics, wave mechanics, hydrodynamic forces, and meteorological data determination; geotechnical data collection and soil mechanics; and stability design procedures. Volume two describes, lists, and illustrates the analysis software. Diskettes containing the software and examples of the software are also included in Volume two.« less

Effective Software Engineering Leadership for Development Programs

ERIC Educational Resources Information Center

Cagle West, Marsha

2010-01-01

Software is a critical component of systems ranging from simple consumer appliances to complex health, nuclear, and flight control systems. The development of quality, reliable, and effective software solutions requires the incorporation of effective software engineering processes and leadership. Processes, approaches, and methodologies for…

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

PubMed Central

Glunčić, Matko; Paar, Vladimir

2013-01-01

The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes). PMID:22977183

Design and implementation of an open source indexing solution for a large set of radiological reports and images.

PubMed

Voet, T; Devolder, P; Pynoo, B; Vercruysse, J; Duyck, P

2007-11-01

This paper hopes to share the insights we experienced during designing, building, and running an indexing solution for a large set of radiological reports and images in a production environment for more than 3 years. Several technical challenges were encountered and solved in the course of this project. One hundred four million words in 1.8 million radiological reports from 1989 to the present were indexed and became instantaneously searchable in a user-friendly fashion; the median query duration is only 31 ms. Currently, our highly tuned index holds 332,088 unique words in four languages. The indexing system is feature-rich and language-independent and allows for making complex queries. For research and training purposes it certainly is a valuable and convenient addition to our radiology informatics toolbox. Extended use of open-source technology dramatically reduced both implementation time and cost. All software we developed related to the indexing project has been made available to the open-source community covered by an unrestricted Berkeley Software Distribution-style license.

Assessment Environment for Complex Systems Software Guide

NASA Technical Reports Server (NTRS)

2013-01-01

This Software Guide (SG) describes the software developed to test the Assessment Environment for Complex Systems (AECS) by the West Virginia High Technology Consortium (WVHTC) Foundation's Mission Systems Group (MSG) for the National Aeronautics and Space Administration (NASA) Aeronautics Research Mission Directorate (ARMD). This software is referred to as the AECS Test Project throughout the remainder of this document. AECS provides a framework for developing, simulating, testing, and analyzing modern avionics systems within an Integrated Modular Avionics (IMA) architecture. The purpose of the AECS Test Project is twofold. First, it provides a means to test the AECS hardware and system developed by MSG. Second, it provides an example project upon which future AECS research may be based. This Software Guide fully describes building, installing, and executing the AECS Test Project as well as its architecture and design. The design of the AECS hardware is described in the AECS Hardware Guide. Instructions on how to configure, build and use the AECS are described in the User's Guide. Sample AECS software, developed by the WVHTC Foundation, is presented in the AECS Software Guide. The AECS Hardware Guide, AECS User's Guide, and AECS Software Guide are authored by MSG. The requirements set forth for AECS are presented in the Statement of Work for the Assessment Environment for Complex Systems authored by NASA Dryden Flight Research Center (DFRC). The intended audience for this document includes software engineers, hardware engineers, project managers, and quality assurance personnel from WVHTC Foundation (the suppliers of the software), NASA (the customer), and future researchers (users of the software). Readers are assumed to have general knowledge in the field of real-time, embedded computer software development.

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

PubMed

Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

2017-07-01

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

Filling the Assurance Gap on Complex Electronics

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Many of the methods used to develop software bare a close resemblance to Complex Electronics (CE) development. CE are now programmed to perform tasks that were previously handled by software, such as communication protocols. For example, the James Webb Space Telescope will use Field Programmable Gate Arrays (FPGAs), which can have over a million logic gates, to send telemetry. System-on-chip (SoC) devices, another type of complex electronics, can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of software-like bugs such as incorrect design, logic, and unexpected interactions within the logic is great. Since CE devices are obscuring the hardware/software boundary, mature software methodologies have been proposed, with slight modifications, to develop these devices. By using standardized S/W Engineering methods such as checklists, missing requirements and bugs can be detected earlier in the development cycle, thus creating a development process for CE that can be easily maintained and configurable based on the device used.

Theoretical and software considerations for general dynamic analysis using multilevel substructured models

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1985-01-01

The dynamic analysis of complex structural systems using the finite element method and multilevel substructured models is presented. The fixed-interface method is selected for substructure reduction because of its efficiency, accuracy, and adaptability to restart and reanalysis. This method is extended to reduction of substructures which are themselves composed of reduced substructures. The implementation and performance of the method in a general purpose software system is emphasized. Solution algorithms consistent with the chosen data structures are presented. It is demonstrated that successful finite element software requires the use of software executives to supplement the algorithmic language. The complexity of the implementation of restart and reanalysis porcedures illustrates the need for executive systems to support the noncomputational aspects of the software. It is shown that significant computational efficiencies can be achieved through proper use of substructuring and reduction technbiques without sacrificing solution accuracy. The restart and reanalysis capabilities and the flexible procedures for multilevel substructured modeling gives economical yet accurate analyses of complex structural systems.

Space Shuttle GN and C Development History and Evolution

NASA Technical Reports Server (NTRS)

Zimpfer, Douglas; Hattis, Phil; Ruppert, John; Gavert, Don

2011-01-01

Completion of the final Space Shuttle flight marks the end of a significant era in Human Spaceflight. Developed in the 1970 s, first launched in 1981, the Space Shuttle embodies many significant engineering achievements. One of these is the development and operation of the first extensive fly-by-wire human space transportation Guidance, Navigation and Control (GN&C) System. Development of the Space Shuttle GN&C represented first time inclusions of modern techniques for electronics, software, algorithms, systems and management in a complex system. Numerous technical design trades and lessons learned continue to drive current vehicle development. For example, the Space Shuttle GN&C system incorporated redundant systems, complex algorithms and flight software rigorously verified through integrated vehicle simulations and avionics integration testing techniques. Over the past thirty years, the Shuttle GN&C continued to go through a series of upgrades to improve safety, performance and to enable the complex flight operations required for assembly of the international space station. Upgrades to the GN&C ranged from the addition of nose wheel steering to modifications that extend capabilities to control of the large flexible configurations while being docked to the Space Station. This paper provides a history of the development and evolution of the Space Shuttle GN&C system. Emphasis is placed on key architecture decisions, design trades and the lessons learned for future complex space transportation system developments. Finally, some of the interesting flight operations experience is provided to inform future developers of flight experiences.

Command-line cellular electrophysiology for conventional and real-time closed-loop experiments.

PubMed

Linaro, Daniele; Couto, João; Giugliano, Michele

2014-06-15

Current software tools for electrophysiological experiments are limited in flexibility and rarely offer adequate support for advanced techniques such as dynamic clamp and hybrid experiments, which are therefore limited to laboratories with a significant expertise in neuroinformatics. We have developed lcg, a software suite based on a command-line interface (CLI) that allows performing both standard and advanced electrophysiological experiments. Stimulation protocols for classical voltage and current clamp experiments are defined by a concise and flexible meta description that allows representing complex waveforms as a piece-wise parametric decomposition of elementary sub-waveforms, abstracting the stimulation hardware. To perform complex experiments lcg provides a set of elementary building blocks that can be interconnected to yield a large variety of experimental paradigms. We present various cellular electrophysiological experiments in which lcg has been employed, ranging from the automated application of current clamp protocols for characterizing basic electrophysiological properties of neurons, to dynamic clamp, response clamp, and hybrid experiments. We finally show how the scripting capabilities behind a CLI are suited for integrating experimental trials into complex workflows, where actual experiment, online data analysis and computational modeling seamlessly integrate. We compare lcg with two open source toolboxes, RTXI and RELACS. We believe that lcg will greatly contribute to the standardization and reproducibility of both simple and complex experiments. Additionally, on the long run the increased efficiency due to a CLI will prove a great benefit for the experimental community. Copyright © 2014 Elsevier B.V. All rights reserved.

GODIVA2: interactive visualization of environmental data on the Web.

PubMed

Blower, J D; Haines, K; Santokhee, A; Liu, C L

2009-03-13

GODIVA2 is a dynamic website that provides visual access to several terabytes of physically distributed, four-dimensional environmental data. It allows users to explore large datasets interactively without the need to install new software or download and understand complex data. Through the use of open international standards, GODIVA2 maintains a high level of interoperability with third-party systems, allowing diverse datasets to be mutually compared. Scientists can use the system to search for features in large datasets and to diagnose the output from numerical simulations and data processing algorithms. Data providers around Europe have adopted GODIVA2 as an INSPIRE-compliant dynamic quick-view system for providing visual access to their data.

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

PubMed Central

2010-01-01

Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service. PMID:21034504

Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data.

PubMed

Schäfer, Christian; Schmidt, Alexander H; Sauter, Jürgen

2017-05-30

Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic stem cell donors, HLA haplotype frequencies of specific populations are used to optimize both donor searches for individual patients and strategic donor registry planning. However, the estimation of haplotype frequencies from HLA genotyping data is challenged by the large amount of genotype data, the complex HLA nomenclature, and the heterogeneous and ambiguous nature of typing records. To meet these challenges, we have developed the open-source software Hapl-o-Mat. It estimates haplotype frequencies from population data including an arbitrary number of loci using an expectation-maximization algorithm. Its key features are the processing of different HLA typing resolutions within a given population sample and the handling of ambiguities recorded via multiple allele codes or genotype list strings. Implemented in C++, Hapl-o-Mat facilitates efficient haplotype frequency estimation from large amounts of genotype data. We demonstrate its accuracy and performance on the basis of artificial and real genotype data. Hapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation. Its capability of processing various forms of HLA genotype data allows for a straightforward haplotype frequency estimation from typing records usually found in stem cell donor registries.

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information.

PubMed

Ristov, Strahil; Brajkovic, Vladimir; Cubric-Curik, Vlatka; Michieli, Ivan; Curik, Ino

2016-09-10

Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan .

Software Fault Tolerance: A Tutorial

NASA Technical Reports Server (NTRS)

Torres-Pomales, Wilfredo

2000-01-01

Because of our present inability to produce error-free software, software fault tolerance is and will continue to be an important consideration in software systems. The root cause of software design errors is the complexity of the systems. Compounding the problems in building correct software is the difficulty in assessing the correctness of software for highly complex systems. After a brief overview of the software development processes, we note how hard-to-detect design faults are likely to be introduced during development and how software faults tend to be state-dependent and activated by particular input sequences. Although component reliability is an important quality measure for system level analysis, software reliability is hard to characterize and the use of post-verification reliability estimates remains a controversial issue. For some applications software safety is more important than reliability, and fault tolerance techniques used in those applications are aimed at preventing catastrophes. Single version software fault tolerance techniques discussed include system structuring and closure, atomic actions, inline fault detection, exception handling, and others. Multiversion techniques are based on the assumption that software built differently should fail differently and thus, if one of the redundant versions fails, it is expected that at least one of the other versions will provide an acceptable output. Recovery blocks, N-version programming, and other multiversion techniques are reviewed.

Weaves as an Interconnection Fabric for ASIM's and Nanosatellites

NASA Technical Reports Server (NTRS)

Gorlick, Michael M.

1995-01-01

Many of the micromachines under consideration require computer support, indeed, one of the appeals of this technology is the ability to intermix mechanical, optical, analog, and digital devices on the same substrate. The amount of computer power is rarely an issue, the sticking point is the complexity of the software required to make effective use of these devices. Micromachines are the nano-technologist's equivalent of 'golden screws'. In other words, they will be piece parts in larger assemblages. For example, a nano-satellite may be composed of stacked silicon wafers where each wafer contains hundreds to thousands of micromachines, digital controllers, general purpose computers, memories, and high-speed bus interconnects. Comparatively few of these devices will be custom designed, most will be stock parts selected from libraries and catalogs. The novelty will lie in the interconnections. For example, a digital accelerometer may be a component part in an adaptive suspension, a monitoring element embedded in the wrapper of a package, or a portion of the smart skin of a launch vehicle. In each case, this device must inter-operate with other devices and probes for the purposes of command, control, and communication. We propose a software technology called 'weaves' that will permit large collections of micromachines and their attendant computers to freely intercommunicate while preserving modularity, transparency, and flexibility. Weaves are composed of networks of communicating software components. The network, and the components comprising it, may be changed even while the software, and the devices it controls, are executing. This unusual degree of software plasticity permits micromachines to dynamically adapt the software to changing conditions and allows system engineers to rapidly and inexpensively develop special purpose software by assembling stock software components in custom configurations.

Component Technology for High-Performance Scientific Simulation Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Epperly, T; Kohn, S; Kumfert, G

2000-11-09

We are developing scientific software component technology to manage the complexity of modem, parallel simulation software and increase the interoperability and re-use of scientific software packages. In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques. We have created a scientific IDL that focuses on the unique interface description needs of scientific codes, such as complex numbers, dense multidimensional arrays, complicated data types, and parallelism. Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for thinking about themore » design of modem object-oriented scientific software libraries. Finally, we also describe a web-based component repository called Alexandria that facilitates the distribution, documentation, and re-use of scientific components and libraries.« less

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales.

PubMed

Rueckl, Martin; Lenzi, Stephen C; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca 2+ -imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca 2+ imaging datasets, particularly when these have been acquired at different spatial scales.

Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Christner, Martin; Dressler, Dirk; Andrian, Mark; Reule, Claudia; Petrini, Orlando

2017-01-01

The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e. g. for outbreak investigations, is often hampered by the complexity of data analysis. We have analysed publicly available MALDI-TOF mass spectra from a large outbreak of Shiga-Toxigenic Escherichia coli in northern Germany using a general purpose software tool for the analysis of complex biological data. The software was challenged with depauperate spectra and reduced learning group sizes to mimic poor spectrum quality and scarcity of reference spectra at the onset of an outbreak. With high quality formic acid extraction spectra, the software's built in classifier accurately identified outbreak related strains using as few as 10 reference spectra (99.8% sensitivity, 98.0% specificity). Selective variation of processing parameters showed impaired marker peak detection and reduced classification accuracy in samples with high background noise or artificially reduced peak counts. However, the software consistently identified mass signals suitable for a highly reliable marker peak based classification approach (100% sensitivity, 99.5% specificity) even from low quality direct deposition spectra. The study demonstrates that general purpose data analysis tools can effectively be used for the analysis of bacterial mass spectra.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales

PubMed Central

Rueckl, Martin; Lenzi, Stephen C.; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W.

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales. PMID:28706482

The Effect of Software Features on Software Adoption and Training in the Audit Profession

ERIC Educational Resources Information Center

Kim, Hyo-Jeong

2012-01-01

Although software has been studied with technology adoption and training research, the study of specific software features for professional groups has been limited. To address this gap, I researched the impact of software features of varying complexity on internal audit (IA) professionals. Two studies along with the development of training…

Bioboxes: standardised containers for interchangeable bioinformatics software.

PubMed

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.

Biocellion: accelerating computer simulation of multicellular biological system models.

PubMed

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 complexity-scalable software-based MPEG-2 video encoder.

PubMed

Chen, Guo-bin; Lu, Xin-ning; Wang, Xing-guo; Liu, Ji-lin

2004-05-01

With the development of general-purpose processors (GPP) and video signal processing algorithms, it is possible to implement a software-based real-time video encoder on GPP, and its low cost and easy upgrade attract developers' interests to transfer video encoding from specialized hardware to more flexible software. In this paper, the encoding structure is set up first to support complexity scalability; then a lot of high performance algorithms are used on the key time-consuming modules in coding process; finally, at programming level, processor characteristics are considered to improve data access efficiency and processing parallelism. Other programming methods such as lookup table are adopted to reduce the computational complexity. Simulation results showed that these ideas could not only improve the global performance of video coding, but also provide great flexibility in complexity regulation.

Simulation-based Testing of Control Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozmen, Ozgur; Nutaro, James J.; Sanyal, Jibonananda

It is impossible to adequately test complex software by examining its operation in a physical prototype of the system monitored. Adequate test coverage can require millions of test cases, and the cost of equipment prototypes combined with the real-time constraints of testing with them makes it infeasible to sample more than a small number of these tests. Model based testing seeks to avoid this problem by allowing for large numbers of relatively inexpensive virtual prototypes that operate in simulation time at a speed limited only by the available computing resources. In this report, we describe how a computer system emulatormore » can be used as part of a model based testing environment; specifically, we show that a complete software stack including operating system and application software - can be deployed within a simulated environment, and that these simulations can proceed as fast as possible. To illustrate this approach to model based testing, we describe how it is being used to test several building control systems that act to coordinate air conditioning loads for the purpose of reducing peak demand. These tests involve the use of ADEVS (A Discrete Event System Simulator) and QEMU (Quick Emulator) to host the operational software within the simulation, and a building model developed with the MODELICA programming language using Buildings Library and packaged as an FMU (Functional Mock-up Unit) that serves as the virtual test environment.« less

New technologies for supporting real-time on-board software development

NASA Astrophysics Data System (ADS)

Kerridge, D.

1995-03-01

The next generation of on-board data management systems will be significantly more complex than current designs, and will be required to perform more complex and demanding tasks in software. Improved hardware technology, in the form of the MA31750 radiation hard processor, is one key component in addressing the needs of future embedded systems. However, to complement these hardware advances, improved support for the design and implementation of real-time data management software is now needed. This will help to control the cost and risk assoicated with developing data management software development as it becomes an increasingly significant element within embedded systems. One particular problem with developing embedded software is managing the non-functional requirements in a systematic way. This paper identifies how Logica has exploited recent developments in hard real-time theory to address this problem through the use of new hard real-time analysis and design methods which can be supported by specialized tools. The first stage in transferring this technology from the research domain to industrial application has already been completed. The MA37150 Hard Real-Time Embedded Software Support Environment (HESSE) is a loosely integrated set of hardware and software tools which directly support the process of hard real-time analysis for software targeting the MA31750 processor. With further development, this HESSE promises to provide embedded system developers with software tools which can reduce the risks associated with developing complex hard real-time software. Supported in this way by more sophisticated software methods and tools, it is foreseen that MA31750 based embedded systems can meet the processing needs for the next generation of on-board data management systems.

The NCI High Performance Computing (HPC) and High Performance Data (HPD) Platform to Support the Analysis of Petascale Environmental Data Collections

NASA Astrophysics Data System (ADS)

Evans, B. J. K.; Pugh, T.; Wyborn, L. A.; Porter, D.; Allen, C.; Smillie, J.; Antony, J.; Trenham, C.; Evans, B. J.; Beckett, D.; Erwin, T.; King, E.; Hodge, J.; Woodcock, R.; Fraser, R.; Lescinsky, D. T.

2014-12-01

The National Computational Infrastructure (NCI) has co-located a priority set of national data assets within a HPC research platform. This powerful in-situ computational platform has been created to help serve and analyse the massive amounts of data across the spectrum of environmental collections - in particular the climate, observational data and geoscientific domains. This paper examines the infrastructure, innovation and opportunity for this significant research platform. NCI currently manages nationally significant data collections (10+ PB) categorised as 1) earth system sciences, climate and weather model data assets and products, 2) earth and marine observations and products, 3) geosciences, 4) terrestrial ecosystem, 5) water management and hydrology, and 6) astronomy, social science and biosciences. The data is largely sourced from the NCI partners (who include the custodians of many of the national scientific records), major research communities, and collaborating overseas organisations. By co-locating these large valuable data assets, new opportunities have arisen by harmonising the data collections, making a powerful transdisciplinary research platformThe data is accessible within an integrated HPC-HPD environment - a 1.2 PFlop supercomputer (Raijin), a HPC class 3000 core OpenStack cloud system and several highly connected large scale and high-bandwidth Lustre filesystems. New scientific software, cloud-scale techniques, server-side visualisation and data services have been harnessed and integrated into the platform, so that analysis is performed seamlessly across the traditional boundaries of the underlying data domains. Characterisation of the techniques along with performance profiling ensures scalability of each software component, all of which can either be enhanced or replaced through future improvements. A Development-to-Operations (DevOps) framework has also been implemented to manage the scale of the software complexity alone. This ensures that software is both upgradable and maintainable, and can be readily reused with complexly integrated systems and become part of the growing global trusted community tools for cross-disciplinary research.

Implementing large projects in software engineering courses

NASA Astrophysics Data System (ADS)

Coppit, David

2006-03-01

In software engineering education, large projects are widely recognized as a useful way of exposing students to the real-world difficulties of team software development. But large projects are difficult to put into practice. First, educators rarely have additional time to manage software projects. Second, classrooms have inherent limitations that threaten the realism of large projects. Third, quantitative evaluation of individuals who work in groups is notoriously difficult. As a result, many software engineering courses compromise the project experience by reducing the team sizes, project scope, and risk. In this paper, we present an approach to teaching a one-semester software engineering course in which 20 to 30 students work together to construct a moderately sized (15KLOC) software system. The approach combines carefully coordinated lectures and homeworks, a hierarchical project management structure, modern communication technologies, and a web-based project tracking and individual assessment system. Our approach provides a more realistic project experience for the students, without incurring significant additional overhead for the instructor. We present our experiences using the approach the last 2 years for the software engineering course at The College of William and Mary. Although the approach has some weaknesses, we believe that they are strongly outweighed by the pedagogical benefits.

The information retrieval system of {open_quotes}heat abd nass transfer{close_quotes} software complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsitsin, A.G.

A project is discussed which is aimed at creating the International Center for certification of software complexes (SC), intended to for soling various heat and mass transfer problems. Information on the experience gained in the operation of an information retrieval SC system is presented.

Towards an Analogue Neuromorphic VLSI Instrument for the Sensing of Complex Odours

NASA Astrophysics Data System (ADS)

Ab Aziz, Muhammad Fazli; Harun, Fauzan Khairi Che; Covington, James A.; Gardner, Julian W.

2011-09-01

Almost all electronic nose instruments reported today employ pattern recognition algorithms written in software and run on digital processors, e.g. micro-processors, microcontrollers or FPGAs. Conversely, in this paper we describe the analogue VLSI implementation of an electronic nose through the design of a neuromorphic olfactory chip. The modelling, design and fabrication of the chip have already been reported. Here a smart interface has been designed and characterised for thisneuromorphic chip. Thus we can demonstrate the functionality of the a VLSI neuromorphic chip, producing differing principal neuron firing patterns to real sensor response data. Further work is directed towards integrating 9 separate neuromorphic chips to create a large neuronal network to solve more complex olfactory problems.

Artificial intelligence support for scientific model-building

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1992-01-01

Scientific model-building can be a time-intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientific development team to understand. We believe that artificial intelligence techniques can facilitate both the model-building and model-sharing process. In this paper, we overview our effort to build a scientific modeling software tool that aids the scientist in developing and using models. This tool includes an interactive intelligent graphical interface, a high-level domain specific modeling language, a library of physics equations and experimental datasets, and a suite of data display facilities.

Optical design methods, applications, and large optics; Proceedings of the Meeting, Hamburg, Federal Republic of Germany, Sept. 19-21, 1988

NASA Astrophysics Data System (ADS)

Masson, Andre; Schulte In den Baeumen, J.; Zuegge, Hannfried

1989-04-01

Recent advances in the design of large optical components are discussed in reviews and reports. Sections are devoted to calculation and optimization methods, optical-design software, IR optics, diagnosis and tolerancing, image formation, lens design, and large optics. Particular attention is given to the use of the pseudoeikonal in optimization, design with nonsequential ray tracing, aspherics and color-correcting elements in the thermal IR, on-line interferometric mirror-deforming measurement with an Ar-ion laser, and the effect of ametropia on laser-interferometric visual acuity. Also discussed are a holographic head-up display for air and ground applications, high-performance objectives for a digital CCD telecine, the optics of the ESO Very Large Telescope, static wavefront correction by Linnik interferometry, and memory-saving techniques in damped least-squares optimization of complex systems.

Autonomous Performance Monitoring System: Monitoring and Self-Tuning (MAST)

NASA Technical Reports Server (NTRS)

Peterson, Chariya; Ziyad, Nigel A.

2000-01-01

Maintaining the long-term performance of software onboard a spacecraft can be a major factor in the cost of operations. In particular, the task of controlling and maintaining a future mission of distributed spacecraft will undoubtedly pose a great challenge, since the complexity of multiple spacecraft flying in formation grows rapidly as the number of spacecraft in the formation increases. Eventually, new approaches will be required in developing viable control systems that can handle the complexity of the data and that are flexible, reliable and efficient. In this paper we propose a methodology that aims to maintain the accuracy of flight software, while reducing the computational complexity of software tuning tasks. The proposed Monitoring and Self-Tuning (MAST) method consists of two parts: a flight software monitoring algorithm and a tuning algorithm. The dependency on the software being monitored is mostly contained in the monitoring process, while the tuning process is a generic algorithm independent of the detailed knowledge on the software. This architecture will enable MAST to be applicable to different onboard software controlling various dynamics of the spacecraft, such as attitude self-calibration, and formation control. An advantage of MAST over conventional techniques such as filter or batch least square is that the tuning algorithm uses machine learning approach to handle uncertainty in the problem domain, resulting in reducing over all computational complexity. The underlying concept of this technique is a reinforcement learning scheme based on cumulative probability generated by the historical performance of the system. The success of MAST will depend heavily on the reinforcement scheme used in the tuning algorithm, which guarantees the tuning solutions exist.

On Quality and Measures in Software Engineering

ERIC Educational Resources Information Center

Bucur, Ion I.

2006-01-01

Complexity measures are mainly used to estimate vital information about reliability and maintainability of software systems from regular analysis of the source code. Such measures also provide constant feedback during a software project to assist the control of the development procedure. There exist several models to classify a software product's…

Introduction: Cybersecurity and Software Assurance Minitrack

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burns, Luanne; George, Richard; Linger, Richard C

Modern society is dependent on software systems of remarkable scope and complexity. Yet methods for assuring their security and functionality have not kept pace. The result is persistent compromises and failures despite best efforts. Cybersecurity methods must work together for situational awareness, attack prevention and detection, threat attribution, minimization of consequences, and attack recovery. Because defective software cannot be secure, assurance technologies must play a central role in cybersecurity approaches. There is increasing recognition of the need for rigorous methods for cybersecurity and software assurance. The goal of this minitrack is to develop science foundations, technologies, and practices that canmore » improve the security and dependability of complex systems.« less

Research of processes of reception and analysis of dynamic digital medical images in hardware/software complexes used for diagnostics and treatment of cardiovascular diseases

NASA Astrophysics Data System (ADS)

Karmazikov, Y. V.; Fainberg, E. M.

2005-06-01

Work with DICOM compatible equipment integrated into hardware and software systems for medical purposes has been considered. Structures of process of reception and translormation of the data are resulted by the example of digital rentgenography and angiography systems, included in hardware-software complex DIMOL-IK. Algorithms of reception and the analysis of the data are offered. Questions of the further processing and storage of the received data are considered.

Initial flight qualification and operational maintenance of X-29A flight software

NASA Technical Reports Server (NTRS)

Earls, Michael R.; Sitz, Joel R.

1989-01-01

A discussion is presented of some significant aspects of the initial flight qualification and operational maintenance of the flight control system softward for the X-29A technology demonstrator. Flight qualification and maintenance of complex, embedded flight control system software poses unique problems. The X-29A technology demonstrator aircraft has a digital flight control system which incorporates functions generally considered too complex for analog systems. Organizational responsibilities, software assurance issues, tools, and facilities are discussed.

What makes computational open source software libraries successful?

NASA Astrophysics Data System (ADS)

Bangerth, Wolfgang; Heister, Timo

2013-01-01

Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

Using CLIPS in the domain of knowledge-based massively parallel programming

NASA Technical Reports Server (NTRS)

Dvorak, Jiri J.

1994-01-01

The Program Development Environment (PDE) is a tool for massively parallel programming of distributed-memory architectures. Adopting a knowledge-based approach, the PDE eliminates the complexity introduced by parallel hardware with distributed memory and offers complete transparency in respect of parallelism exploitation. The knowledge-based part of the PDE is realized in CLIPS. Its principal task is to find an efficient parallel realization of the application specified by the user in a comfortable, abstract, domain-oriented formalism. A large collection of fine-grain parallel algorithmic skeletons, represented as COOL objects in a tree hierarchy, contains the algorithmic knowledge. A hybrid knowledge base with rule modules and procedural parts, encoding expertise about application domain, parallel programming, software engineering, and parallel hardware, enables a high degree of automation in the software development process. In this paper, important aspects of the implementation of the PDE using CLIPS and COOL are shown, including the embedding of CLIPS with C++-based parts of the PDE. The appropriateness of the chosen approach and of the CLIPS language for knowledge-based software engineering are discussed.

IDEAL: Images Across Domains, Experiments, Algorithms and Learning

NASA Astrophysics Data System (ADS)

Ushizima, Daniela M.; Bale, Hrishikesh A.; Bethel, E. Wes; Ercius, Peter; Helms, Brett A.; Krishnan, Harinarayan; Grinberg, Lea T.; Haranczyk, Maciej; Macdowell, Alastair A.; Odziomek, Katarzyna; Parkinson, Dilworth Y.; Perciano, Talita; Ritchie, Robert O.; Yang, Chao

2016-11-01

Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this paper, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

Data Standards for Flow Cytometry

PubMed Central

SPIDLEN, JOSEF; GENTLEMAN, ROBERT C.; HAALAND, PERRY D.; LANGILLE, MORGAN; MEUR, NOLWENN LE; OCHS, MICHAEL F.; SCHMITT, CHARLES; SMITH, CLAYTON A.; TREISTER, ADAM S.; BRINKMAN, RYAN R.

2009-01-01

Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture the full scope of FCM experiments and there is a demand for software tools that can assist in the exploration and analysis of large FCM datasets. We are implementing a standardized approach to capturing, analyzing, and disseminating FCM data that will facilitate both more complex analyses and analysis of datasets that could not previously be efficiently studied. Initial work has focused on developing a community-based guideline for recording and reporting the details of FCM experiments. Open source software tools that implement this standard are being created, with an emphasis on facilitating reproducible and extensible data analyses. As well, tools for electronic collaboration will assist the integrated access and comprehension of experiments to empower users to collaborate on FCM analyses. This coordinated, joint development of bioinformatics standards and software tools for FCM data analysis has the potential to greatly facilitate both basic and clinical research—impacting a notably diverse range of medical and environmental research areas. PMID:16901228

DynamO: a free O(N) general event-driven molecular dynamics simulator.

PubMed

Bannerman, M N; Sargant, R; Lue, L

2011-11-30

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. Copyright © 2011 Wiley Periodicals, Inc.

Redefining the genetics of Murine Gammaherpesvirus 68 via transcriptome-based annotation

PubMed Central

Johnson, L. Steven; Willert, Erin K.; Virgin, Herbert W.

2010-01-01

Summary Viral genetic studies often focus on large open reading frames (ORFs) identified during genome annotation (ORF-based annotation). Here we provide a tool and software set for defining gene expression by murine gammaherpesvirus 68 (γHV68) nucleotide-by-nucleotide across the 119,450 basepair (bp) genome. These tools allowed us to determine that viral RNA expression was significantly more complex than predicted from ORF-based annotation, including over 73,000 nucleotides of unexpected transcription within 30 expressed genomic regions (EGRs). Approximately 90% of this RNA expression was antisense to genomic regions containing known large ORFs. We verified the existence of novel transcripts in three EGRs using standard methods to validate the approach and determined which parts of the transcriptome depend on protein or viral DNA synthesis. This redefines the genetic map of γHV68, indicates that herpesviruses contain significantly more genetic complexity than predicted from ORF-based genome annotations, and provides new tools and approaches for viral genetic studies. PMID:20542255

A Virtual Reality Visualization Tool for Neuron Tracing

PubMed Central

Usher, Will; Klacansky, Pavol; Federer, Frederick; Bremer, Peer-Timo; Knoll, Aaron; Angelucci, Alessandra; Pascucci, Valerio

2017-01-01

Tracing neurons in large-scale microscopy data is crucial to establishing a wiring diagram of the brain, which is needed to understand how neural circuits in the brain process information and generate behavior. Automatic techniques often fail for large and complex datasets, and connectomics researchers may spend weeks or months manually tracing neurons using 2D image stacks. We present a design study of a new virtual reality (VR) system, developed in collaboration with trained neuroanatomists, to trace neurons in microscope scans of the visual cortex of primates. We hypothesize that using consumer-grade VR technology to interact with neurons directly in 3D will help neuroscientists better resolve complex cases and enable them to trace neurons faster and with less physical and mental strain. We discuss both the design process and technical challenges in developing an interactive system to navigate and manipulate terabyte-sized image volumes in VR. Using a number of different datasets, we demonstrate that, compared to widely used commercial software, consumer-grade VR presents a promising alternative for scientists. PMID:28866520

Review of integrated digital systems: evolution and adoption

NASA Astrophysics Data System (ADS)

Fritz, Lawrence W.

The factors that are influencing the evolution of photogrammetric and remote sensing technology to transition into fully integrated digital systems are reviewed. These factors include societal pressures for new, more timely digital products from the Spatial Information Sciencesand the adoption of rapid technological advancements in digital processing hardware and software. Current major developments in leading government mapping agencies of the USA, such as the Digital Production System (DPS) modernization programme at the Defense Mapping Agency, and the Automated Nautical Charting System II (ANCS-II) programme and Integrated Digital Photogrammetric Facility (IDPF) at NOAA/National Ocean Service, illustrate the significant benefits to be realized. These programmes are examples of different levels of integrated systems that have been designed to produce digital products. They provide insights to the management complexities to be considered for very large integrated digital systems. In recognition of computer industry trends, a knowledge-based architecture for managing the complexity of the very large spatial information systems of the future is proposed.

A Virtual Reality Visualization Tool for Neuron Tracing.

PubMed

Usher, Will; Klacansky, Pavol; Federer, Frederick; Bremer, Peer-Timo; Knoll, Aaron; Yarch, Jeff; Angelucci, Alessandra; Pascucci, Valerio

2018-01-01

Tracing neurons in large-scale microscopy data is crucial to establishing a wiring diagram of the brain, which is needed to understand how neural circuits in the brain process information and generate behavior. Automatic techniques often fail for large and complex datasets, and connectomics researchers may spend weeks or months manually tracing neurons using 2D image stacks. We present a design study of a new virtual reality (VR) system, developed in collaboration with trained neuroanatomists, to trace neurons in microscope scans of the visual cortex of primates. We hypothesize that using consumer-grade VR technology to interact with neurons directly in 3D will help neuroscientists better resolve complex cases and enable them to trace neurons faster and with less physical and mental strain. We discuss both the design process and technical challenges in developing an interactive system to navigate and manipulate terabyte-sized image volumes in VR. Using a number of different datasets, we demonstrate that, compared to widely used commercial software, consumer-grade VR presents a promising alternative for scientists.

AnClim and ProClimDB software for data quality control and homogenization of time series

NASA Astrophysics Data System (ADS)

Stepanek, Petr

2015-04-01

During the last decade, a software package consisting of AnClim, ProClimDB and LoadData for processing (mainly climatological) data has been created. This software offers a complex solution for processing of climatological time series, starting from loading the data from a central database (e.g. Oracle, software LoadData), through data duality control and homogenization to time series analysis, extreme value evaluations and RCM outputs verification and correction (ProClimDB and AnClim software). The detection of inhomogeneities is carried out on a monthly scale through the application of AnClim, or newly by R functions called from ProClimDB, while quality control, the preparation of reference series and the correction of found breaks is carried out by the ProClimDB software. The software combines many statistical tests, types of reference series and time scales (monthly, seasonal and annual, daily and sub-daily ones). These can be used to create an "ensemble" of solutions, which may be more reliable than any single method. AnClim software is suitable for educational purposes: e.g. for students getting acquainted with methods used in climatology. Built-in graphical tools and comparison of various statistical tests help in better understanding of a given method. ProClimDB is, on the contrary, tool aimed for processing of large climatological datasets. Recently, functions from R may be used within the software making it more efficient in data processing and capable of easy inclusion of new methods (when available under R). An example of usage is easy comparison of methods for correction of inhomogeneities in daily data (HOM of Paul Della-Marta, SPLIDHOM method of Olivier Mestre, DAP - own method, QM of Xiaolan Wang and others). The software is available together with further information on www.climahom.eu . Acknowledgement: this work was partially funded by the project "Building up a multidisciplinary scientific team focused on drought" No. CZ.1.07/2.3.00/20.0248.

Design and demonstration of automated data analysis algorithms for ultrasonic inspection of complex composite panels with bonds

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Forsyth, David S.; Welter, John T.

2016-02-01

To address the data review burden and improve the reliability of the ultrasonic inspection of large composite structures, automated data analysis (ADA) algorithms have been developed to make calls on indications that satisfy the detection criteria and minimize false calls. The original design followed standard procedures for analyzing signals for time-of-flight indications and backwall amplitude dropout. However, certain complex panels with varying shape, ply drops and the presence of bonds can complicate this interpretation process. In this paper, enhancements to the automated data analysis algorithms are introduced to address these challenges. To estimate the thickness of the part and presence of bonds without prior information, an algorithm tracks potential backwall or bond-line signals, and evaluates a combination of spatial, amplitude, and time-of-flight metrics to identify bonded sections. Once part boundaries, thickness transitions and bonded regions are identified, feature extraction algorithms are applied to multiple sets of through-thickness and backwall C-scan images, for evaluation of both first layer through thickness and layers under bonds. ADA processing results are presented for a variety of complex test specimens with inserted materials and other test discontinuities. Lastly, enhancements to the ADA software interface are presented, which improve the software usability for final data review by the inspectors and support the certification process.

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.

PubMed

Sorzano, Carlos Oscar S; de la Rosa-Trevín, José Miguel; Tama, Florence; Jonić, Slavica

2014-11-01

This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction. Copyright © 2014 Elsevier Inc. All rights reserved.

Experiences in integrating auto-translated state-chart designs for model checking

NASA Technical Reports Server (NTRS)

Pingree, P. J.; Benowitz, E. G.

2003-01-01

In the complex environment of JPL's flight missions with increasing dependency on advanced software designs, traditional software validation methods of simulation and testing are being stretched to adequately cover the needs of software development.

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

2005-04-01

The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

DTIC Science & Technology

2015-08-01

Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten and James P Larentzos Approved for...Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten Weapons and Materials Research Directorate, ARL James P Larentzos Engility...Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software 5a. CONTRACT NUMBER 5b

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

NASA Astrophysics Data System (ADS)

Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

2017-02-01

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

Strategies for concurrent processing of complex algorithms in data driven architectures

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Mielke, Roland R.

1988-01-01

The purpose is to document research to develop strategies for concurrent processing of complex algorithms in data driven architectures. The problem domain consists of decision-free algorithms having large-grained, computationally complex primitive operations. Such are often found in signal processing and control applications. The anticipated multiprocessor environment is a data flow architecture containing between two and twenty computing elements. Each computing element is a processor having local program memory, and which communicates with a common global data memory. A new graph theoretic model called ATAMM which establishes rules for relating a decomposed algorithm to its execution in a data flow architecture is presented. The ATAMM model is used to determine strategies to achieve optimum time performance and to develop a system diagnostic software tool. In addition, preliminary work on a new multiprocessor operating system based on the ATAMM specifications is described.

Efficient Construction of Discrete Adjoint Operators on Unstructured Grids by Using Complex Variables

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Kleb, William L.

2005-01-01

A methodology is developed and implemented to mitigate the lengthy software development cycle typically associated with constructing a discrete adjoint solver for aerodynamic simulations. The approach is based on a complex-variable formulation that enables straightforward differentiation of complicated real-valued functions. An automated scripting process is used to create the complex-variable form of the set of discrete equations. An efficient method for assembling the residual and cost function linearizations is developed. The accuracy of the implementation is verified through comparisons with a discrete direct method as well as a previously developed handcoded discrete adjoint approach. Comparisons are also shown for a large-scale configuration to establish the computational efficiency of the present scheme. To ultimately demonstrate the power of the approach, the implementation is extended to high temperature gas flows in chemical nonequilibrium. Finally, several fruitful research and development avenues enabled by the current work are suggested.

Efficient Construction of Discrete Adjoint Operators on Unstructured Grids Using Complex Variables

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Kleb, William L.

2005-01-01

A methodology is developed and implemented to mitigate the lengthy software development cycle typically associated with constructing a discrete adjoint solver for aerodynamic simulations. The approach is based on a complex-variable formulation that enables straightforward differentiation of complicated real-valued functions. An automated scripting process is used to create the complex-variable form of the set of discrete equations. An efficient method for assembling the residual and cost function linearizations is developed. The accuracy of the implementation is verified through comparisons with a discrete direct method as well as a previously developed handcoded discrete adjoint approach. Comparisons are also shown for a large-scale configuration to establish the computational efficiency of the present scheme. To ultimately demonstrate the power of the approach, the implementation is extended to high temperature gas flows in chemical nonequilibrium. Finally, several fruitful research and development avenues enabled by the current work are suggested.

Visualizing Parallel Computer System Performance

NASA Technical Reports Server (NTRS)

Malony, Allen D.; Reed, Daniel A.

1988-01-01

Parallel computer systems are among the most complex of man's creations, making satisfactory performance characterization difficult. Despite this complexity, there are strong, indeed, almost irresistible, incentives to quantify parallel system performance using a single metric. The fallacy lies in succumbing to such temptations. A complete performance characterization requires not only an analysis of the system's constituent levels, it also requires both static and dynamic characterizations. Static or average behavior analysis may mask transients that dramatically alter system performance. Although the human visual system is remarkedly adept at interpreting and identifying anomalies in false color data, the importance of dynamic, visual scientific data presentation has only recently been recognized Large, complex parallel system pose equally vexing performance interpretation problems. Data from hardware and software performance monitors must be presented in ways that emphasize important events while eluding irrelevant details. Design approaches and tools for performance visualization are the subject of this paper.

Gray: a ray tracing-based Monte Carlo simulator for PET.

PubMed

Freese, David L; Olcott, Peter D; Buss, Samuel R; Levin, Craig S

2018-05-21

Monte Carlo simulation software plays a critical role in PET system design. Performing complex, repeated Monte Carlo simulations can be computationally prohibitive, as even a single simulation can require a large amount of time and a computing cluster to complete. Here we introduce Gray, a Monte Carlo simulation software for PET systems. Gray exploits ray tracing methods used in the computer graphics community to greatly accelerate simulations of PET systems with complex geometries. We demonstrate the implementation of models for positron range, annihilation acolinearity, photoelectric absorption, Compton scatter, and Rayleigh scatter. For validation, we simulate the GATE PET benchmark, and compare energy, distribution of hits, coincidences, and run time. We show a [Formula: see text] speedup using Gray, compared to GATE for the same simulation, while demonstrating nearly identical results. We additionally simulate the Siemens Biograph mCT system with both the NEMA NU-2 scatter phantom and sensitivity phantom. We estimate the total sensitivity within [Formula: see text]% when accounting for differences in peak NECR. We also estimate the peak NECR to be [Formula: see text] kcps, or within [Formula: see text]% of published experimental data. The activity concentration of the peak is also estimated within 1.3%.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

PubMed

Misirli, Göksel; Nguyen, Tramy; McLaughlin, James Alastair; Vaidyanathan, Prashant; Jones, Timothy S; Densmore, Douglas; Myers, Chris; Wipat, Anil

2018-06-05

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.

[USE OF LASER RAMAN-LUMINESCENT TECHNOLOGIES FOR EVALUATION OF QUALITY OF MEAT PRODUCTS AND DETERMINATION OF THE DEGREE OF THEIR BACTERIAL CONTAMINATION].

PubMed

Kukushkin, V I; Satusheva, E V; Aleksandrov, M T; Morozova, O A; Pashkov, E P; Ambartsumyan, O A; Amosova, V A

2015-01-01

Determination of the effect of microorganisms on spoilage of meat products during various temperature regimes of storage by integral indexes of luminescent lines in their spectra and development of an algorithm of microorganism indication by an express method using laser Raman-luminescent spectroscopy. Minced meat from beef and pork was used. Determination of quantity of mesophilic aerobic and opportunistic-anaerobic microorganisms was carried out by serial 10-fold dilutions with subsequent parallel seeding into Rida count total 24 plates and Petri dishes with 5% blood agar. Sample study was carried out in luminescent software-hardware complex Enspectr L405 (a variant of Enspectr M software-hardware complexes). Meat spoilage was established to be caused to a large degree by Pseudomonas genus (P. fluorescens, P. putida, P. fragi et al.) bacterial growth. Raman-luminescent spectra of bacteria that compose microflora, characterizing and accompanying beef and pork spoilage, were measured and recorded into a database. The results obtained will allow to use this technique in the future for both express-indication and differentiation of microorganisms and express-evaluation of quality of meat products at all stages of their manufacturing, storage, transport and realization.

Viewpoints: Interactive Exploration of Large Multivariate Earth and Space Science Data Sets

NASA Astrophysics Data System (ADS)

Levit, C.; Gazis, P. R.

2006-05-01

Analysis and visualization of extremely large and complex data sets may be one of the most significant challenges facing earth and space science investigators in the forthcoming decades. While advances in hardware speed and storage technology have roughly kept up with (indeed, have driven) increases in database size, the same is not of our abilities to manage the complexity of these data. Current missions, instruments, and simulations produce so much data of such high dimensionality that they outstrip the capabilities of traditional visualization and analysis software. This problem can only be expected to get worse as data volumes increase by orders of magnitude in future missions and in ever-larger supercomputer simulations. For large multivariate data (more than 105 samples or records with more than 5 variables per sample) the interactive graphics response of most existing statistical analysis, machine learning, exploratory data analysis, and/or visualization tools such as Torch, MLC++, Matlab, S++/R, and IDL stutters, stalls, or stops working altogether. Fortunately, the graphics processing units (GPUs) built in to all professional desktop and laptop computers currently on the market are capable of transforming, filtering, and rendering hundreds of millions of points per second. We present a prototype open-source cross-platform application which leverages much of the power latent in the GPU to enable smooth interactive exploration and analysis of large high- dimensional data using a variety of classical and recent techniques. The targeted application is the interactive analysis of large, complex, multivariate data sets, with dimensionalities that may surpass 100 and sample sizes that may exceed 106-108.

Identification of Factors That Affect Software Complexity.

ERIC Educational Resources Information Center

Kaiser, Javaid

A survey of computer scientists was conducted to identify factors that affect software complexity. A total of 160 items were selected from the literature to include in a questionnaire sent to 425 individuals who were employees of computer-related businesses in Lawrence and Kansas City. The items were grouped into nine categories called system…

You Cannot Do This Alone! Increasing Task Interdependence in Cooperative Educational Videogames to Encourage Collaboration

ERIC Educational Resources Information Center

Nebel, Steve; Schneider, Sascha; Beege, Maik; Kolda, Franziska; Mackiewicz, Valerie; Rey, Günter Daniel

2017-01-01

Complex, multimedia software such as educational videogames offer a wide range of elements to modify learner behavior. The adjustment of such software might support learning, especially in complex settings like collaborative or cooperative scenarios. Coming from a theoretical background of educational psychology, our experiment seeks to implement…

MiniWall Tool for Analyzing CFD and Wind Tunnel Large Data Sets

NASA Technical Reports Server (NTRS)

Schuh, Michael J.; Melton, John E.; Stremel, Paul M.

2017-01-01

It is challenging to review and assimilate large data sets created by Computational Fluid Dynamics (CFD) simulations and wind tunnel tests. Over the past 10 years, NASA Ames Research Center has developed and refined a software tool dubbed the MiniWall to increase productivity in reviewing and understanding large CFD-generated data sets. Under the recent NASA ERA project, the application of the tool expanded to enable rapid comparison of experimental and computational data. The MiniWall software is browser based so that it runs on any computer or device that can display a web page. It can also be used remotely and securely by using web server software such as the Apache HTTP server. The MiniWall software has recently been rewritten and enhanced to make it even easier for analysts to review large data sets and extract knowledge and understanding from these data sets. This paper describes the MiniWall software and demonstrates how the different features are used to review and assimilate large data sets.

MiniWall Tool for Analyzing CFD and Wind Tunnel Large Data Sets

NASA Technical Reports Server (NTRS)

Schuh, Michael J.; Melton, John E.; Stremel, Paul M.

2017-01-01

It is challenging to review and assimilate large data sets created by Computational Fluid Dynamics (CFD) simulations and wind tunnel tests. Over the past 10 years, NASA Ames Research Center has developed and refined a software tool dubbed the "MiniWall" to increase productivity in reviewing and understanding large CFD-generated data sets. Under the recent NASA ERA project, the application of the tool expanded to enable rapid comparison of experimental and computational data. The MiniWall software is browser based so that it runs on any computer or device that can display a web page. It can also be used remotely and securely by using web server software such as the Apache HTTP Server. The MiniWall software has recently been rewritten and enhanced to make it even easier for analysts to review large data sets and extract knowledge and understanding from these data sets. This paper describes the MiniWall software and demonstrates how the different features are used to review and assimilate large data sets.

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

PubMed

Gallicchio, Emilio; Xia, Junchao; Flynn, William F; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M

2015-11-01

Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications

NASA Astrophysics Data System (ADS)

Pascal, Bruce D.; West, Graham M.; Scharager-Tapia, Catherina; Flefil, Ricardo; Moroni, Tina; Martinez-Acedo, Pablo; Griffin, Patrick R.; Carvalloza, Anthony C.

2015-12-01

The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS1 data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS1 data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS2 analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com .

Test Driven Development of a Parameterized Ice Sheet Component

NASA Astrophysics Data System (ADS)

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.

Playing with Plug-ins

ERIC Educational Resources Information Center

Thompson, Douglas E.

2013-01-01

In today's complex music software packages, many features can remain unexplored and unused. Software plug-ins--available in most every music software package, yet easily overlooked in the software's basic operations--are one such feature. In this article, I introduce readers to plug-ins and offer tips for purchasing plug-ins I have…

bioboxes v510

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barton, Michael; Droge, Johannes; Belmann, Peter

2017-06-22

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. The developers propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

Polyglot Programming in Applications Used for Genetic Data Analysis

PubMed Central

Nowak, Robert M.

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

Multimission Software Reuse in an Environment of Large Paradigm Shifts

NASA Technical Reports Server (NTRS)

Wilson, Robert K.

1996-01-01

The ground data systems provided for NASA space mission support are discussed. As space missions expand, the ground systems requirements become more complex. Current ground data systems provide for telemetry, command, and uplink and downlink processing capabilities. The new millennium project (NMP) technology testbed for 21st century NASA missions is discussed. The program demonstrates spacecraft and ground system technologies. The paradigm shift from detailed ground sequencing to a goal oriented planning approach is considered. The work carried out to meet this paradigm for the Deep Space-1 (DS-1) mission is outlined.

Polyglot programming in applications used for genetic data analysis.

PubMed

Nowak, Robert M

2014-01-01

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

Enhanced job control language procedures for the SIMSYS2D two-dimensional water-quality simulation system

USGS Publications Warehouse

Karavitis, G.A.

1984-01-01

The SIMSYS2D two-dimensional water-quality simulation system is a large-scale digital modeling software system used to simulate flow and transport of solutes in freshwater and estuarine environments. Due to the size, processing requirements, and complexity of the system, there is a need to easily move the system and its associated files between computer sites when required. A series of job control language (JCL) procedures was written to allow transferability between IBM and IBM-compatible computers. (USGS)

Ontology-Driven Information Integration

NASA Technical Reports Server (NTRS)

Tissot, Florence; Menzel, Chris

2005-01-01

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

DIY 3D printing of custom orthopaedic implants: a proof of concept study.

PubMed

Frame, Mark; Leach, William

2014-03-01

3D printing is an emerging technology that is primarily used for aiding the design and prototyping of implants. As this technology has evolved it has now become possible to produce functional and definitive implants manufactured using a 3D printing process. This process, however, previously required a large financial investment in complex machinery and professionals skilled in 3D product design. Our pilot study's aim was to design and create a 3D printed custom orthopaedic implant using only freely available consumer hardware and software.

Big Data Analytics in Medicine and Healthcare.

PubMed

Ristevski, Blagoj; Chen, Ming

2018-05-10

This paper surveys big data with highlighting the big data analytics in medicine and healthcare. Big data characteristics: value, volume, velocity, variety, veracity and variability are described. Big data analytics in medicine and healthcare covers integration and analysis of large amount of complex heterogeneous data such as various - omics data (genomics, epigenomics, transcriptomics, proteomics, metabolomics, interactomics, pharmacogenomics, diseasomics), biomedical data and electronic health records data. We underline the challenging issues about big data privacy and security. Regarding big data characteristics, some directions of using suitable and promising open-source distributed data processing software platform are given.

CSM Testbed Development and Large-Scale Structural Applications

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Gillian, R. E.; Mccleary, Susan L.; Lotts, C. G.; Poole, E. L.; Overman, A. L.; Macy, S. C.

1989-01-01

A research activity called Computational Structural Mechanics (CSM) conducted at the NASA Langley Research Center is described. This activity is developing advanced structural analysis and computational methods that exploit high-performance computers. Methods are developed in the framework of the CSM Testbed software system and applied to representative complex structural analysis problems from the aerospace industry. An overview of the CSM Testbed methods development environment is presented and some new numerical methods developed on a CRAY-2 are described. Selected application studies performed on the NAS CRAY-2 are also summarized.

THE EPA MULTIMEDIA INTEGRATED MODELING SYSTEM SOFTWARE SUITE

EPA Science Inventory

The U.S. EPA is developing a Multimedia Integrated Modeling System (MIMS) framework that will provide a software infrastructure or environment to support constructing, composing, executing, and evaluating complex modeling studies. The framework will include (1) common software ...

Implications of Aggregated DoD Information Systems for Information Assurance Certification and Accreditation

DTIC Science & Technology

2010-01-01

offshoring, or producing major software components overseas (Defense Science Board, 2009). These trends raise concerns about the level of trust that...7 Software Complexity...7 Increasing Software Vulnerabilities and Malware Population . . . . . . . . . . . . . . . . 9 Limitations of

Complexity: an internet resource for analysis of DNA sequence complexity

PubMed Central

Orlov, Y. L.; Potapov, V. N.

2004-01-01

The search for DNA regions with low complexity is one of the pivotal tasks of modern structural analysis of complete genomes. The low complexity may be preconditioned by strong inequality in nucleotide content (biased composition), by tandem or dispersed repeats or by palindrome-hairpin structures, as well as by a combination of all these factors. Several numerical measures of textual complexity, including combinatorial and linguistic ones, together with complexity estimation using a modified Lempel–Ziv algorithm, have been implemented in a software tool called ‘Complexity’ (http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/). The software enables a user to search for low-complexity regions in long sequences, e.g. complete bacterial genomes or eukaryotic chromosomes. In addition, it estimates the complexity of groups of aligned sequences. PMID:15215465

What Not To Do: Anti-patterns for Developing Scientific Workflow Software Components

NASA Astrophysics Data System (ADS)

Futrelle, J.; Maffei, A. R.; Sosik, H. M.; Gallager, S. M.; York, A.

2013-12-01

Scientific workflows promise to enable efficient scaling-up of researcher code to handle large datasets and workloads, as well as documentation of scientific processing via standardized provenance records, etc. Workflow systems and related frameworks for coordinating the execution of otherwise separate components are limited, however, in their ability to overcome software engineering design problems commonly encountered in pre-existing components, such as scripts developed externally by scientists in their laboratories. In practice, this often means that components must be rewritten or replaced in a time-consuming, expensive process. In the course of an extensive workflow development project involving large-scale oceanographic image processing, we have begun to identify and codify 'anti-patterns'--problematic design characteristics of software--that make components fit poorly into complex automated workflows. We have gone on to develop and document low-effort solutions and best practices that efficiently address the anti-patterns we have identified. The issues, solutions, and best practices can be used to evaluate and improve existing code, as well as guiding the development of new components. For example, we have identified a common anti-pattern we call 'batch-itis' in which a script fails and then cannot perform more work, even if that work is not precluded by the failure. The solution we have identified--removing unnecessary looping over independent units of work--is often easier to code than the anti-pattern, as it eliminates the need for complex control flow logic in the component. Other anti-patterns we have identified are similarly easy to identify and often easy to fix. We have drawn upon experience working with three science teams at Woods Hole Oceanographic Institution, each of which has designed novel imaging instruments and associated image analysis code. By developing use cases and prototypes within these teams, we have undertaken formal evaluations of software components developed by programmers with widely varying levels of expertise, and have been able to discover and characterize a number of anti-patterns. Our evaluation methodology and testbed have also enabled us to assess the efficacy of strategies to address these anti-patterns according to scientifically relevant metrics, such as ability of algorithms to perform faster than the rate of data acquisition and the accuracy of workflow component output relative to ground truth. The set of anti-patterns and solutions we have identified augments of the body of more well-known software engineering anti-patterns by addressing additional concerns that obtain when a software component has to function as part of a workflow assembled out of independently-developed codebases. Our experience shows that identifying and resolving these anti-patterns reduces development time and improves performance without reducing component reusability.

Interactive exploration of coastal restoration modeling in virtual environments

NASA Astrophysics Data System (ADS)

Gerndt, Andreas; Miller, Robert; Su, Simon; Meselhe, Ehab; Cruz-Neira, Carolina

2009-02-01

Over the last decades, Louisiana has lost a substantial part of its coastal region to the Gulf of Mexico. The goal of the project depicted in this paper is to investigate the complex ecological and geophysical system not only to find solutions to reverse this development but also to protect the southern landscape of Louisiana for disastrous impacts of natural hazards like hurricanes. This paper sets a focus on the interactive data handling of the Chenier Plain which is only one scenario of the overall project. The challenge addressed is the interactive exploration of large-scale time-depending 2D simulation results and of terrain data with a high resolution that is available for this region. Besides data preparation, efficient visualization approaches optimized for the usage in virtual environments are presented. These are embedded in a complex framework for scientific visualization of time-dependent large-scale datasets. To provide a straightforward interface for rapid application development, a software layer called VRFlowVis has been developed. Several architectural aspects to encapsulate complex virtual reality aspects like multi-pipe vs. cluster-based rendering are discussed. Moreover, the distributed post-processing architecture is investigated to prove its efficiency for the geophysical domain. Runtime measurements conclude this paper.

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos

PubMed Central

Giurumescu, Claudiu A.; Kang, Sukryool; Planchon, Thomas A.; Betzig, Eric; Bloomekatz, Joshua; Yelon, Deborah; Cosman, Pamela; Chisholm, Andrew D.

2012-01-01

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking. PMID:23052905

CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations.

PubMed

Wang, Xihong; Zheng, Zhuqing; Cai, Yudong; Chen, Ting; Li, Chao; Fu, Weiwei; Jiang, Yu

2017-12-01

The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of nonhuman genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data. The computational speed of CNVcaller was 1-2 orders of magnitude faster than CNVnator and Genome STRiP for complex genomes with thousands of unmapped scaffolds. CNV detection of 232 goats required only 1.4 days on a single compute node. Additionally, the Mendelian consistency of sheep trios indicated that CNVcaller mitigated the influence of high proportions of gaps and misassembled duplications in the nonhuman reference genome assembly. Furthermore, multiple evaluations using real sheep and human data indicated that CNVcaller achieved the best accuracy and sensitivity for detecting duplications. The fast generalized detection algorithms included in CNVcaller overcome prior computational barriers for detecting CNVs in large-scale sequencing data with complex genomic structures. Therefore, CNVcaller promotes population genetic analyses of functional CNVs in more species. © The Authors 2017. Published by Oxford University Press.

CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations

PubMed Central

Wang, Xihong; Zheng, Zhuqing; Cai, Yudong; Chen, Ting; Li, Chao; Fu, Weiwei

2017-01-01

Abstract Background The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of nonhuman genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Results Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data. The computational speed of CNVcaller was 1–2 orders of magnitude faster than CNVnator and Genome STRiP for complex genomes with thousands of unmapped scaffolds. CNV detection of 232 goats required only 1.4 days on a single compute node. Additionally, the Mendelian consistency of sheep trios indicated that CNVcaller mitigated the influence of high proportions of gaps and misassembled duplications in the nonhuman reference genome assembly. Furthermore, multiple evaluations using real sheep and human data indicated that CNVcaller achieved the best accuracy and sensitivity for detecting duplications. Conclusions The fast generalized detection algorithms included in CNVcaller overcome prior computational barriers for detecting CNVs in large-scale sequencing data with complex genomic structures. Therefore, CNVcaller promotes population genetic analyses of functional CNVs in more species. PMID:29220491

Adapting iterative algorithms for solving large sparse linear systems for efficient use on the CDC CYBER 205

NASA Technical Reports Server (NTRS)

Kincaid, D. R.; Young, D. M.

1984-01-01

Adapting and designing mathematical software to achieve optimum performance on the CYBER 205 is discussed. Comments and observations are made in light of recent work done on modifying the ITPACK software package and on writing new software for vector supercomputers. The goal was to develop very efficient vector algorithms and software for solving large sparse linear systems using iterative methods.

Supporting Source Code Comprehension during Software Evolution and Maintenance

ERIC Educational Resources Information Center

Alhindawi, Nouh

2013-01-01

This dissertation addresses the problems of program comprehension to support the evolution of large-scale software systems. The research concerns how software engineers locate features and concepts along with categorizing changes within very large bodies of source code along with their versioned histories. More specifically, advanced Information…

A Predictive Approach to Eliminating Errors in Software Code

NASA Technical Reports Server (NTRS)

2006-01-01

NASA s Metrics Data Program Data Repository is a database that stores problem, product, and metrics data. The primary goal of this data repository is to provide project data to the software community. In doing so, the Metrics Data Program collects artifacts from a large NASA dataset, generates metrics on the artifacts, and then generates reports that are made available to the public at no cost. The data that are made available to general users have been sanitized and authorized for publication through the Metrics Data Program Web site by officials representing the projects from which the data originated. The data repository is operated by NASA s Independent Verification and Validation (IV&V) Facility, which is located in Fairmont, West Virginia, a high-tech hub for emerging innovation in the Mountain State. The IV&V Facility was founded in 1993, under the NASA Office of Safety and Mission Assurance, as a direct result of recommendations made by the National Research Council and the Report of the Presidential Commission on the Space Shuttle Challenger Accident. Today, under the direction of Goddard Space Flight Center, the IV&V Facility continues its mission to provide the highest achievable levels of safety and cost-effectiveness for mission-critical software. By extending its data to public users, the facility has helped improve the safety, reliability, and quality of complex software systems throughout private industry and other government agencies. Integrated Software Metrics, Inc., is one of the organizations that has benefited from studying the metrics data. As a result, the company has evolved into a leading developer of innovative software-error prediction tools that help organizations deliver better software, on time and on budget.

NASA Data Acquisition System Software Development for Rocket Propulsion Test Facilities

NASA Technical Reports Server (NTRS)

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 to achieve using LabVIEW. The

Optically buffered Jones-matrix-based multifunctional optical coherence tomography with polarization mode dispersion correction

PubMed Central

Hong, Young-Joo; Makita, Shuichi; Sugiyama, Satoshi; Yasuno, Yoshiaki

2014-01-01

Polarization mode dispersion (PMD) degrades the performance of Jones-matrix-based polarization-sensitive multifunctional optical coherence tomography (JM-OCT). The problem is specially acute for optically buffered JM-OCT, because the long fiber in the optical buffering module induces a large amount of PMD. This paper aims at presenting a method to correct the effect of PMD in JM-OCT. We first mathematically model the PMD in JM-OCT and then derive a method to correct the PMD. This method is a combination of simple hardware modification and subsequent software correction. The hardware modification is introduction of two polarizers which transform the PMD into global complex modulation of Jones matrix. Subsequently, the software correction demodulates the global modulation. The method is validated with an experimentally obtained point spread function with a mirror sample, as well as by in vivo measurement of a human retina. PMID:25657888

The center for causal discovery of biomedical knowledge from big data

PubMed Central

Bahar, Ivet; Becich, Michael J; Benos, Panayiotis V; Berg, Jeremy; Espino, Jeremy U; Glymour, Clark; Jacobson, Rebecca Crowley; Kienholz, Michelle; Lee, Adrian V; Lu, Xinghua; Scheines, Richard

2015-01-01

The Big Data to Knowledge (BD2K) Center for Causal Discovery is developing and disseminating an integrated set of open source tools that support causal modeling and discovery of biomedical knowledge from large and complex biomedical datasets. The Center integrates teams of biomedical and data scientists focused on the refinement of existing and the development of new constraint-based and Bayesian algorithms based on causal Bayesian networks, the optimization of software for efficient operation in a supercomputing environment, and the testing of algorithms and software developed using real data from 3 representative driving biomedical projects: cancer driver mutations, lung disease, and the functional connectome of the human brain. Associated training activities provide both biomedical and data scientists with the knowledge and skills needed to apply and extend these tools. Collaborative activities with the BD2K Consortium further advance causal discovery tools and integrate tools and resources developed by other centers. PMID:26138794

Rule-Based Design of Plant Expression Vectors Using GenoCAD.

PubMed

Coll, Anna; Wilson, Mandy L; Gruden, Kristina; Peccoud, Jean

2015-01-01

Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.

Hadoop distributed batch processing for Gaia: a success story

NASA Astrophysics Data System (ADS)

Riello, Marco

2015-12-01

The DPAC Cambridge Data Processing Centre (DPCI) is responsible for the photometric calibration of the Gaia data including the low resolution spectra. The large data volume produced by Gaia (~26 billion transits/year), the complexity of its data stream and the self-calibrating approach pose unique challenges for scalability, reliability and robustness of both the software pipelines and the operations infrastructure. DPCI has been the first in DPAC to realise the potential of Hadoop and Map/Reduce and to adopt them as the core technologies for its infrastructure. This has proven a winning choice allowing DPCI unmatched processing throughput and reliability within DPAC to the point that other DPCs have started following our footsteps. In this talk we will present the software infrastructure developed to build the distributed and scalable batch data processing system that is currently used in production at DPCI and the excellent results in terms of performance of the system.

FAME, a microprocessor based front-end analysis and modeling environment

NASA Technical Reports Server (NTRS)

Rosenbaum, J. D.; Kutin, E. B.

1980-01-01

Higher order software (HOS) is a methodology for the specification and verification of large scale, complex, real time systems. The HOS methodology was implemented as FAME (front end analysis and modeling environment), a microprocessor based system for interactively developing, analyzing, and displaying system models in a low cost user-friendly environment. The nature of the model is such that when completed it can be the basis for projection to a variety of forms such as structured design diagrams, Petri-nets, data flow diagrams, and PSL/PSA source code. The user's interface with the analyzer is easily recognized by any current user of a structured modeling approach; therefore extensive training is unnecessary. Furthermore, when all the system capabilities are used one can check on proper usage of data types, functions, and control structures thereby adding a new dimension to the design process that will lead to better and more easily verified software designs.

Mapping RNA-seq Reads with STAR

PubMed Central

Dobin, Alexander; Gingeras, Thomas R.

2015-01-01

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, signal visualization, and so forth. In this unit we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is Open Source software that can be run on Unix, Linux or Mac OS X systems. PMID:26334920

Mapping RNA-seq Reads with STAR.

PubMed

Dobin, Alexander; Gingeras, Thomas R

2015-09-03

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. Copyright © 2015 John Wiley & Sons, Inc.

Multivariate statistical analysis software technologies for astrophysical research involving large data bases

NASA Technical Reports Server (NTRS)

Djorgovski, George

1993-01-01

The existing and forthcoming data bases from NASA missions contain an abundance of information whose complexity cannot be efficiently tapped with simple statistical techniques. Powerful multivariate statistical methods already exist which can be used to harness much of the richness of these data. Automatic classification techniques have been developed to solve the problem of identifying known types of objects in multiparameter data sets, in addition to leading to the discovery of new physical phenomena and classes of objects. We propose an exploratory study and integration of promising techniques in the development of a general and modular classification/analysis system for very large data bases, which would enhance and optimize data management and the use of human research resource.

Multivariate statistical analysis software technologies for astrophysical research involving large data bases

NASA Technical Reports Server (NTRS)

Djorgovski, Stanislav

1992-01-01

The existing and forthcoming data bases from NASA missions contain an abundance of information whose complexity cannot be efficiently tapped with simple statistical techniques. Powerful multivariate statistical methods already exist which can be used to harness much of the richness of these data. Automatic classification techniques have been developed to solve the problem of identifying known types of objects in multi parameter data sets, in addition to leading to the discovery of new physical phenomena and classes of objects. We propose an exploratory study and integration of promising techniques in the development of a general and modular classification/analysis system for very large data bases, which would enhance and optimize data management and the use of human research resources.

ERP (enterprise resource planning) systems can streamline healthcare business functions.

PubMed

Jenkins, E K; Christenson, E

2001-05-01

Enterprise resource planning (ERP) software applications are designed to facilitate the systemwide integration of complex processes and functions across a large enterprise consisting of many internal and external constituents. Although most currently available ERP applications generally are tailored to the needs of the manufacturing industry, many large healthcare systems are investigating these applications. Due to the significant differences between manufacturing and patient care, ERP-based systems do not easily translate to the healthcare setting. In particular, the lack of clinical standardization impedes the use of ERP systems for clinical integration. Nonetheless, an ERP-based system can help a healthcare organization integrate many functions, including patient scheduling, human resources management, workload forecasting, and management of workflow, that are not directly dependent on clinical decision making.

Intelligent Systems and Advanced User Interfaces for Design, Operation, and Maintenance of Command Management Systems

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1998-01-01

Historically Command Management Systems (CMS) have been large, expensive, spacecraft-specific software systems that were costly to build, operate, and maintain. Current and emerging hardware, software, and user interface technologies may offer an opportunity to facilitate the initial formulation and design of a spacecraft-specific CMS as well as a to develop a more generic or a set of core components for CMS systems. Current MOC (mission operations center) hardware and software include Unix workstations, the C/C++ and Java programming languages, and X and Java window interfaces representations. This configuration provides the power and flexibility to support sophisticated systems and intelligent user interfaces that exploit state-of-the-art technologies in human-machine systems engineering, decision making, artificial intelligence, and software engineering. One of the goals of this research is to explore the extent to which technologies developed in the research laboratory can be productively applied in a complex system such as spacecraft command management. Initial examination of some of the issues in CMS design and operation suggests that application of technologies such as intelligent planning, case-based reasoning, design and analysis tools from a human-machine systems engineering point of view (e.g., operator and designer models) and human-computer interaction tools, (e.g., graphics, visualization, and animation), may provide significant savings in the design, operation, and maintenance of a spacecraft-specific CMS as well as continuity for CMS design and development across spacecraft with varying needs. The savings in this case is in software reuse at all stages of the software engineering process.

Simulating the behavior of volatiles belonging to the C-O-H-S system in silicate melts under magmatic conditions with the software D-Compress

NASA Astrophysics Data System (ADS)

Burgisser, Alain; Alletti, Marina; Scaillet, Bruno

2015-06-01

Modeling magmatic degassing, or how the volatile distribution between gas and melt changes at pressure varies, is a complex task that involves a large number of thermodynamical relationships and that requires dedicated software. This article presents the software D-Compress, which computes the gas and melt volatile composition of five element sets in magmatic systems (O-H, S-O-H, C-S-O-H, C-S-O-H-Fe, and C-O-H). It has been calibrated so as to simulate the volatiles coexisting with three common types of silicate melts (basalt, phonolite, and rhyolite). Operational temperatures depend on melt composition and range from 790 to 1400 °C. A specificity of D-Compress is the calculation of volatile composition as pressure varies along a (de)compression path between atmospheric and 3000 bars. This software was prepared so as to maximize versatility by proposing different sets of input parameters. In particular, whenever new solubility laws on specific melt compositions are available, the model parameters can be easily tuned to run the code on that composition. Parameter gaps were minimized by including sets of chemical species for which calibration data were available over a wide range of pressure, temperature, and melt composition. A brief description of the model rationale is followed by the presentation of the software capabilities. Examples of use are then presented with outputs comparisons between D-Compress and other currently available thermodynamical models. The compiled software and the source code are available as electronic supplementary materials.

Towards Test Driven Development for Computational Science with pFUnit

NASA Technical Reports Server (NTRS)

Rilee, Michael L.; Clune, Thomas L.

2014-01-01

Developers working in Computational Science & Engineering (CSE)/High Performance Computing (HPC) must contend with constant change due to advances in computing technology and science. Test Driven Development (TDD) is a methodology that mitigates software development risks due to change at the cost of adding comprehensive and continuous testing to the development process. Testing frameworks tailored for CSE/HPC, like pFUnit, can lower the barriers to such testing, yet CSE software faces unique constraints foreign to the broader software engineering community. Effective testing of numerical software requires a comprehensive suite of oracles, i.e., use cases with known answers, as well as robust estimates for the unavoidable numerical errors associated with implementation with finite-precision arithmetic. At first glance these concerns often seem exceedingly challenging or even insurmountable for real-world scientific applications. However, we argue that this common perception is incorrect and driven by (1) a conflation between model validation and software verification and (2) the general tendency in the scientific community to develop relatively coarse-grained, large procedures that compound numerous algorithmic steps.We believe TDD can be applied routinely to numerical software if developers pursue fine-grained implementations that permit testing, neatly side-stepping concerns about needing nontrivial oracles as well as the accumulation of errors. We present an example of a successful, complex legacy CSE/HPC code whose development process shares some aspects with TDD, which we contrast with current and potential capabilities. A mix of our proposed methodology and framework support should enable everyday use of TDD by CSE-expert developers.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

From, by, and for the OSSD: Software Engineering Education Using an Open Source Software Approach

ERIC Educational Resources Information Center

Huang, Kun; Dong, Yifei; Ge, Xun

2006-01-01

Computing is a complex, multidisciplinary field that requires a range of professional proficiencies. Computing students are expected to develop in-depth knowledge and skills, integrate and apply their knowledge flexibly to solve complex problems, and work successfully in teams. However, many students who graduate with degrees in computing fail to…

The Evolution of Software Publication in Astronomy

NASA Astrophysics Data System (ADS)

Cantiello, Matteo

2018-01-01

Software is a fundamental component of the scientific research process. As astronomical discoveries increasingly rely on complex numerical calculations and the analysis of big data sets, publishing and documenting software is a fundamental step in ensuring transparency and reproducibility of results. I will briefly discuss the recent history of software publication and highlight the challenges and opportunities ahead.

The Evolution of Software Pricing: From Box Licenses to Application Service Provider Models.

ERIC Educational Resources Information Center

Bontis, Nick; Chung, Honsan

2000-01-01

Describes three different pricing models for software. Findings of this case study support the proposition that software pricing is a complex and subjective process. The key determinant of alignment between vendor and user is the nature of value in the software to the buyer. This value proposition may range from increased cost reduction to…

bioNerDS: exploring bioinformatics’ database and software use through literature mining

PubMed Central

2013-01-01

Background Biology-focused databases and software define bioinformatics and their use is central to computational biology. In such a complex and dynamic field, it is of interest to understand what resources are available, which are used, how much they are used, and for what they are used. While scholarly literature surveys can provide some insights, large-scale computer-based approaches to identify mentions of bioinformatics databases and software from primary literature would automate systematic cataloguing, facilitate the monitoring of usage, and provide the foundations for the recovery of computational methods for analysing biological data, with the long-term aim of identifying best/common practice in different areas of biology. Results We have developed bioNerDS, a named entity recogniser for the recovery of bioinformatics databases and software from primary literature. We identify such entities with an F-measure ranging from 63% to 91% at the mention level and 63-78% at the document level, depending on corpus. Not attaining a higher F-measure is mostly due to high ambiguity in resource naming, which is compounded by the on-going introduction of new resources. To demonstrate the software, we applied bioNerDS to full-text articles from BMC Bioinformatics and Genome Biology. General mention patterns reflect the remit of these journals, highlighting BMC Bioinformatics’s emphasis on new tools and Genome Biology’s greater emphasis on data analysis. The data also illustrates some shifts in resource usage: for example, the past decade has seen R and the Gene Ontology join BLAST and GenBank as the main components in bioinformatics processing. Abstract Conclusions We demonstrate the feasibility of automatically identifying resource names on a large-scale from the scientific literature and show that the generated data can be used for exploration of bioinformatics database and software usage. For example, our results help to investigate the rate of change in resource usage and corroborate the suspicion that a vast majority of resources are created, but rarely (if ever) used thereafter. bioNerDS is available at http://bionerds.sourceforge.net/. PMID:23768135

eddy4R 0.2.0: a DevOps model for community-extensible processing and analysis of eddy-covariance data based on R, Git, Docker, and HDF5

NASA Astrophysics Data System (ADS)

Metzger, Stefan; Durden, David; Sturtevant, Cove; Luo, Hongyan; Pingintha-Durden, Natchaya; Sachs, Torsten; Serafimovich, Andrei; Hartmann, Jörg; Li, Jiahong; Xu, Ke; Desai, Ankur R.

2017-08-01

Large differences in instrumentation, site setup, data format, and operating system stymie the adoption of a universal computational environment for processing and analyzing eddy-covariance (EC) data. This results in limited software applicability and extensibility in addition to often substantial inconsistencies in flux estimates. Addressing these concerns, this paper presents the systematic development of portable, reproducible, and extensible EC software achieved by adopting a development and systems operation (DevOps) approach. This software development model is used for the creation of the eddy4R family of EC code packages in the open-source R language for statistical computing. These packages are community developed, iterated via the Git distributed version control system, and wrapped into a portable and reproducible Docker filesystem that is independent of the underlying host operating system. The HDF5 hierarchical data format then provides a streamlined mechanism for highly compressed and fully self-documented data ingest and output. The usefulness of the DevOps approach was evaluated for three test applications. First, the resultant EC processing software was used to analyze standard flux tower data from the first EC instruments installed at a National Ecological Observatory (NEON) field site. Second, through an aircraft test application, we demonstrate the modular extensibility of eddy4R to analyze EC data from other platforms. Third, an intercomparison with commercial-grade software showed excellent agreement (R2 = 1.0 for CO2 flux). In conjunction with this study, a Docker image containing the first two eddy4R packages and an executable example workflow, as well as first NEON EC data products are released publicly. We conclude by describing the work remaining to arrive at the automated generation of science-grade EC fluxes and benefits to the science community at large. This software development model is applicable beyond EC and more generally builds the capacity to deploy complex algorithms developed by scientists in an efficient and scalable manner. In addition, modularity permits meeting project milestones while retaining extensibility with time.

Collaboratively Architecting a Scalable and Adaptable Petascale Infrastructure to Support Transdisciplinary Scientific Research for the Australian Earth and Environmental Sciences

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Evans, B. J. K.; Pugh, T.; Lescinsky, D. T.; Foster, C.; Uhlherr, A.

2014-12-01

The National Computational Infrastructure (NCI) at the Australian National University (ANU) is a partnership between CSIRO, ANU, Bureau of Meteorology (BoM) and Geoscience Australia. Recent investments in a 1.2 PFlop Supercomputer (Raijin), ~ 20 PB data storage using Lustre filesystems and a 3000 core high performance cloud have created a hybrid platform for higher performance computing and data-intensive science to enable large scale earth and climate systems modelling and analysis. There are > 3000 users actively logging in and > 600 projects on the NCI system. Efficiently scaling and adapting data and software systems to petascale infrastructures requires the collaborative development of an architecture that is designed, programmed and operated to enable users to interactively invoke different forms of in-situ computation over complex and large scale data collections. NCI makes available major and long tail data collections from both the government and research sectors based on six themes: 1) weather, climate and earth system science model simulations, 2) marine and earth observations, 3) geosciences, 4) terrestrial ecosystems, 5) water and hydrology and 6) astronomy, bio and social. Collectively they span the lithosphere, crust, biosphere, hydrosphere, troposphere, and stratosphere. Collections are the operational form for data management and access. Similar data types from individual custodians are managed cohesively. Use of international standards for discovery and interoperability allow complex interactions within and between the collections. This design facilitates a transdisciplinary approach to research and enables a shift from small scale, 'stove-piped' science efforts to large scale, collaborative systems science. This new and complex infrastructure requires a move to shared, globally trusted software frameworks that can be maintained and updated. Workflow engines become essential and need to integrate provenance, versioning, traceability, repeatability and publication. There are also human resource challenges as highly skilled HPC/HPD specialists, specialist programmers, and data scientists are required whose skills can support scaling to the new paradigm of effective and efficient data-intensive earth science analytics on petascale, and soon to be exascale systems.

Data flow modeling techniques

NASA Technical Reports Server (NTRS)

Kavi, K. M.

1984-01-01

There have been a number of simulation packages developed for the purpose of designing, testing and validating computer systems, digital systems and software systems. Complex analytical tools based on Markov and semi-Markov processes have been designed to estimate the reliability and performance of simulated systems. Petri nets have received wide acceptance for modeling complex and highly parallel computers. In this research data flow models for computer systems are investigated. Data flow models can be used to simulate both software and hardware in a uniform manner. Data flow simulation techniques provide the computer systems designer with a CAD environment which enables highly parallel complex systems to be defined, evaluated at all levels and finally implemented in either hardware or software. Inherent in data flow concept is the hierarchical handling of complex systems. In this paper we will describe how data flow can be used to model computer system.

Software engineering the mixed model for genome-wide association studies on large samples.

PubMed

Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

2009-11-01

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

Use of a quality improvement tool, the prioritization matrix, to identify and prioritize triage software algorithm enhancement.

PubMed

North, Frederick; Varkey, Prathiba; Caraballo, Pedro; Vsetecka, Darlene; Bartel, Greg

2007-10-11

Complex decision support software can require significant effort in maintenance and enhancement. A quality improvement tool, the prioritization matrix, was successfully used to guide software enhancement of algorithms in a symptom assessment call center.

Complexity Measure for the Prototype System Description Language (PSDL)

DTIC Science & Technology

2002-06-01

Albrecht, A. and Gaffney , J., Software Function Source Lines of Code and Development Effort Prediction, IEEE Transactions on Software Engineering...Through Meausrement”; Proceedings of the IEEE, Vol. 77, No. 4, April 89. Schach, Stephen, R., Software Engineering, Second Edition, IRWIN, Burr Ridge

Evolution of Flexible Multibody Dynamics for Simulation Applications Supporting Human Spaceflight

NASA Technical Reports Server (NTRS)

Huynh, An; Brain, Thomas A.; MacLean, John R.; Quiocho, Leslie J.

2016-01-01

During the course of transition from the Space Shuttle and International Space Station programs to the Orion and Journey to Mars exploration programs, a generic flexible multibody dynamics formulation and associated software implementation has evolved to meet an ever changing set of requirements at the NASA Johnson Space Center (JSC). Challenging problems related to large transitional topologies and robotic free-flyer vehicle capture/ release, contact dynamics, and exploration missions concept evaluation through simulation (e.g., asteroid surface operations) have driven this continued development. Coupled with this need is the requirement to oftentimes support human spaceflight operations in real-time. Moreover, it has been desirable to allow even more rapid prototyping of on-orbit manipulator and spacecraft systems, to support less complex infrastructure software for massively integrated simulations, to yield further computational efficiencies, and to take advantage of recent advances and availability of multi-core computing platforms. Since engineering analysis, procedures development, and crew familiarity/training for human spaceflight is fundamental to JSC's charter, there is also a strong desire to share and reuse models in both the non-realtime and real-time domains, with the goal of retaining as much multibody dynamics fidelity as possible. Three specific enhancements are reviewed here: (1) linked list organization to address large transitional topologies, (2) body level model order reduction, and (3) parallel formulation/implementation. This paper provides a detailed overview of these primary updates to JSC's flexible multibody dynamics algorithms as well as a comparison of numerical results to previous formulations and associated software.

Navigating the fifth dimension: new concepts in interactive multimodality and multidimensional image navigation

NASA Astrophysics Data System (ADS)

Ratib, Osman; Rosset, Antoine; Dahlbom, Magnus; Czernin, Johannes

2005-04-01

Display and interpretation of multi dimensional data obtained from the combination of 3D data acquired from different modalities (such as PET-CT) require complex software tools allowing the user to navigate and modify the different image parameters. With faster scanners it is now possible to acquire dynamic images of a beating heart or the transit of a contrast agent adding a fifth dimension to the data. We developed a DICOM-compliant software for real time navigation in very large sets of 5 dimensional data based on an intuitive multidimensional jog-wheel widely used by the video-editing industry. The software, provided under open source licensing, allows interactive, single-handed, navigation through 3D images while adjusting blending of image modalities, image contrast and intensity and the rate of cine display of dynamic images. In this study we focused our effort on the user interface and means for interactively navigating in these large data sets while easily and rapidly changing multiple parameters such as image position, contrast, intensity, blending of colors, magnification etc. Conventional mouse-driven user interface requiring the user to manipulate cursors and sliders on the screen are too cumbersome and slow. We evaluated several hardware devices and identified a category of multipurpose jogwheel device that is used in the video-editing industry that is particularly suitable for rapidly navigating in five dimensions while adjusting several display parameters interactively. The application of this tool will be demonstrated in cardiac PET-CT imaging and functional cardiac MRI studies.

Numerical simulation and optimization of casting process for complex pump

NASA Astrophysics Data System (ADS)

Liu, Xueqin; Dong, Anping; Wang, Donghong; Lu, Yanling; Zhu, Guoliang

2017-09-01

The complex shape of the casting pump body has large complicated structure and uniform wall thickness, which easy give rise to casting defects. The numerical simulation software ProCAST is used to simulate the initial top gating process, after analysis of the material and structure characteristics of the high-pressure pump. The filling process was overall smooth, not there the water shortage phenomenon. But the circular shrinkage defects appear at the bottom of casting during solidification process. Then, the casting parameters were optimized and adding cold iron in the bottom. The shrinkage weight was reduced from 0.00167g to 0.0005g. The porosity volume was reduced from 1.39cm3 to 0.41cm3. The optimization scheme is simulated and actual experimented. The defect has been significantly improved.

High-frequency CAD-based scattering model: SERMAT

NASA Astrophysics Data System (ADS)

Goupil, D.; Boutillier, M.

1991-09-01

Specifications for an industrial radar cross section (RCS) calculation code are given: it must be able to exchange data with many computer aided design (CAD) systems, it must be fast, and it must have powerful graphic tools. Classical physical optics (PO) and equivalent currents (EC) techniques have proven their efficiency on simple objects for a long time. Difficult geometric problems occur when objects with very complex shapes have to be computed. Only a specific geometric code can solve these problems. We have established that, once these problems have been solved: (1) PO and EC give good results on complex objects of large size compared to wavelength; and (2) the implementation of these objects in a software package (SERMAT) allows fast and sufficiently precise domain RCS calculations to meet industry requirements in the domain of stealth.

Automatic high-throughput screening of colloidal crystals using machine learning

NASA Astrophysics Data System (ADS)

Spellings, Matthew; Glotzer, Sharon C.

Recent improvements in hardware and software have united to pose an interesting problem for computational scientists studying self-assembly of particles into crystal structures: while studies covering large swathes of parameter space can be dispatched at once using modern supercomputers and parallel architectures, identifying the different regions of a phase diagram is often a serial task completed by hand. While analytic methods exist to distinguish some simple structures, they can be difficult to apply, and automatic identification of more complex structures is still lacking. In this talk we describe one method to create numerical ``fingerprints'' of local order and use them to analyze a study of complex ordered structures. We can use these methods as first steps toward automatic exploration of parameter space and, more broadly, the strategic design of new materials.

Software Framework for Development of Web-GIS Systems for Analysis of Georeferenced Geophysical Data

NASA Astrophysics Data System (ADS)

Okladnikov, I.; Gordov, E. P.; Titov, A. G.

2011-12-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, remote sensing products, etc.) are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated software framework for rapid development of providing such support information-computational systems based on Web-GIS technologies has been created. The software framework consists of 3 basic parts: computational kernel developed using ITTVIS Interactive Data Language (IDL), a set of PHP-controllers run within specialized web portal, and JavaScript class library for development of typical components of web mapping application graphical user interface (GUI) based on AJAX technology. Computational kernel comprise of number of modules for datasets access, mathematical and statistical data analysis and visualization of results. Specialized web-portal consists of web-server Apache, complying OGC standards Geoserver software which is used as a base for presenting cartographical information over the Web, and a set of PHP-controllers implementing web-mapping application logic and governing computational kernel. JavaScript library aiming at graphical user interface development is based on GeoExt library combining ExtJS Framework and OpenLayers software. Based on the software framework an information-computational system for complex analysis of large georeferenced data archives was developed. Structured environmental datasets available for processing now include two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, meteorological observational data for the territory of the former USSR for the 20th century, and others. Current version of the system is already involved into a scientific research process. Particularly, recently the system was successfully used for analysis of Siberia climate changes and its impact in the region. The software framework presented allows rapid development of Web-GIS systems for geophysical data analysis thus providing specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. This work is partially supported by RFBR grants #10-07-00547, #11-05-01190, and SB RAS projects 4.31.1.5, 4.31.2.7, 4, 8, 9, 50 and 66.

Software-hardware complex for the input of telemetric information obtained from rocket studies of the radiation of the earth's upper atmosphere

NASA Astrophysics Data System (ADS)

Bazdrov, I. I.; Bortkevich, V. S.; Khokhlov, V. N.

2004-10-01

This paper describes a software-hardware complex for the input into a personal computer of telemetric information obtained by means of telemetry stations TRAL KR28, RTS-8, and TRAL K2N. Structural and functional diagrams are given of the input device and the hardware complex. Results that characterize the features of the input process and selective data of optical measurements of atmospheric radiation are given. © 2004

Rule-based modeling with Virtual Cell

PubMed Central

Schaff, James C.; Vasilescu, Dan; Moraru, Ion I.; Loew, Leslie M.; Blinov, Michael L.

2016-01-01

Summary: Rule-based modeling is invaluable when the number of possible species and reactions in a model become too large to allow convenient manual specification. The popular rule-based software tools BioNetGen and NFSim provide powerful modeling and simulation capabilities at the cost of learning a complex scripting language which is used to specify these models. Here, we introduce a modeling tool that combines new graphical rule-based model specification with existing simulation engines in a seamless way within the familiar Virtual Cell (VCell) modeling environment. A mathematical model can be built integrating explicit reaction networks with reaction rules. In addition to offering a large choice of ODE and stochastic solvers, a model can be simulated using a network free approach through the NFSim simulation engine. Availability and implementation: Available as VCell (versions 6.0 and later) at the Virtual Cell web site (http://vcell.org/). The application installs and runs on all major platforms and does not require registration for use on the user’s computer. Tutorials are available at the Virtual Cell website and Help is provided within the software. Source code is available at Sourceforge. Contact: vcell_support@uchc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27497444

Tri-track: free software for large-scale particle tracking.

PubMed

Vallotton, Pascal; Olivier, Sandra

2013-04-01

The ability to correctly track objects in time-lapse sequences is important in many applications of microscopy. Individual object motions typically display a level of dynamic regularity reflecting the existence of an underlying physics or biology. Best results are obtained when this local information is exploited. Additionally, if the particle number is known to be approximately constant, a large number of tracking scenarios may be rejected on the basis that they are not compatible with a known maximum particle velocity. This represents information of a global nature, which should ideally be exploited too. Some time ago, we devised an efficient algorithm that exploited both types of information. The tracking task was reduced to a max-flow min-cost problem instance through a novel graph structure that comprised vertices representing objects from three consecutive image frames. The algorithm is explained here for the first time. A user-friendly implementation is provided, and the specific relaxation mechanism responsible for the method's effectiveness is uncovered. The software is particularly competitive for complex dynamics such as dense antiparallel flows, or in situations where object displacements are considerable. As an application, we characterize a remarkable vortex structure formed by bacteria engaged in interstitial motility.

Some Thoughts Regarding Practical Quantum Computing

NASA Astrophysics Data System (ADS)

Ghoshal, Debabrata; Gomez, Richard; Lanzagorta, Marco; Uhlmann, Jeffrey

2006-03-01

Quantum computing has become an important area of research in computer science because of its potential to provide more efficient algorithmic solutions to certain problems than are possible with classical computing. The ability of performing parallel operations over an exponentially large computational space has proved to be the main advantage of the quantum computing model. In this regard, we are particularly interested in the potential applications of quantum computers to enhance real software systems of interest to the defense, industrial, scientific and financial communities. However, while much has been written in popular and scientific literature about the benefits of the quantum computational model, several of the problems associated to the practical implementation of real-life complex software systems in quantum computers are often ignored. In this presentation we will argue that practical quantum computation is not as straightforward as commonly advertised, even if the technological problems associated to the manufacturing and engineering of large-scale quantum registers were solved overnight. We will discuss some of the frequently overlooked difficulties that plague quantum computing in the areas of memories, I/O, addressing schemes, compilers, oracles, approximate information copying, logical debugging, error correction and fault-tolerant computing protocols.

Managing a tier-2 computer centre with a private cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, Stefano; Berzano, Dario; Brunetti, Riccardo; Lusso, Stefano; Vallero, Sara

2014-06-01

In a typical scientific computing centre, several applications coexist and share a single physical infrastructure. An underlying Private Cloud infrastructure eases the management and maintenance of such heterogeneous applications (such as multipurpose or application-specific batch farms, Grid sites, interactive data analysis facilities and others), allowing dynamic allocation resources to any application. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques. Such infrastructures are being deployed in some large centres (see e.g. the CERN Agile Infrastructure project), but with several open-source tools reaching maturity this is becoming viable also for smaller sites. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 centre, an Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The private cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem and the OpenWRT Linux distribution (used for network virtualization); a future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and OCCI.

Technology survey on video face tracking

NASA Astrophysics Data System (ADS)

Zhang, Tong; Gomes, Herman Martins

2014-03-01

With the pervasiveness of monitoring cameras installed in public areas, schools, hospitals, work places and homes, video analytics technologies for interpreting these video contents are becoming increasingly relevant to people's lives. Among such technologies, human face detection and tracking (and face identification in many cases) are particularly useful in various application scenarios. While plenty of research has been conducted on face tracking and many promising approaches have been proposed, there are still significant challenges in recognizing and tracking people in videos with uncontrolled capturing conditions, largely due to pose and illumination variations, as well as occlusions and cluttered background. It is especially complex to track and identify multiple people simultaneously in real time due to the large amount of computation involved. In this paper, we present a survey on literature and software that are published or developed during recent years on the face tracking topic. The survey covers the following topics: 1) mainstream and state-of-the-art face tracking methods, including features used to model the targets and metrics used for tracking; 2) face identification and face clustering from face sequences; and 3) software packages or demonstrations that are available for algorithm development or trial. A number of publically available databases for face tracking are also introduced.

Hybrid PV/diesel solar power system design using multi-level factor analysis optimization

NASA Astrophysics Data System (ADS)

Drake, Joshua P.

Solar power systems represent a large area of interest across a spectrum of organizations at a global level. It was determined that a clear understanding of current state of the art software and design methods, as well as optimization methods, could be used to improve the design methodology. Solar power design literature was researched for an in depth understanding of solar power system design methods and algorithms. Multiple software packages for the design and optimization of solar power systems were analyzed for a critical understanding of their design workflow. In addition, several methods of optimization were studied, including brute force, Pareto analysis, Monte Carlo, linear and nonlinear programming, and multi-way factor analysis. Factor analysis was selected as the most efficient optimization method for engineering design as it applied to solar power system design. The solar power design algorithms, software work flow analysis, and factor analysis optimization were combined to develop a solar power system design optimization software package called FireDrake. This software was used for the design of multiple solar power systems in conjunction with an energy audit case study performed in seven Tibetan refugee camps located in Mainpat, India. A report of solar system designs for the camps, as well as a proposed schedule for future installations was generated. It was determined that there were several improvements that could be made to the state of the art in modern solar power system design, though the complexity of current applications is significant.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

PubMed Central

Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R.; Smith, Jeremy C.; Kasson, Peter M.; van der Spoel, David; Hess, Berk; Lindahl, Erik

2013-01-01

Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23407358

Next generation lightweight mirror modeling software

NASA Astrophysics Data System (ADS)

Arnold, William R.; Fitzgerald, Matthew; Rosa, Rubin Jaca; Stahl, H. Philip

2013-09-01

The advances in manufacturing techniques for lightweight mirrors, such as EXELSIS deep core low temperature fusion, Corning's continued improvements in the Frit bonding process and the ability to cast large complex designs, combined with water-jet and conventional diamond machining of glasses and ceramics has created the need for more efficient means of generating finite element models of these structures. Traditional methods of assembling 400,000 + element models can take weeks of effort, severely limiting the range of possible optimization variables. This paper will introduce model generation software developed under NASA sponsorship for the design of both terrestrial and space based mirrors. The software deals with any current mirror manufacturing technique, single substrates, multiple arrays of substrates, as well as the ability to merge submodels into a single large model. The modeler generates both mirror and suspension system elements, suspensions can be created either for each individual petal or the whole mirror. A typical model generation of 250,000 nodes and 450,000 elements only takes 3-5 minutes, much of that time being variable input time. The program can create input decks for ANSYS, ABAQUS and NASTRAN. An archive/retrieval system permits creation of complete trade studies, varying cell size, depth, and petal size, suspension geometry with the ability to recall a particular set of parameters and make small or large changes with ease. The input decks created by the modeler are text files which can be modified by any text editor, all the shell thickness parameters and suspension spring rates are accessible and comments in deck identify which groups of elements are associated with these parameters. This again makes optimization easier. With ANSYS decks, the nodes representing support attachments are grouped into components; in ABAQUS these are SETS and in NASTRAN as GRIDPOINT SETS, this make integration of these models into large telescope or satellite models easier.

Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust.

PubMed

Božičević, Alen; Dobrzyński, Maciej; De Bie, Hans; Gafner, Frank; Garo, Eliane; Hamburger, Matthias

2017-12-05

The technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.

Rule-based modeling and simulations of the inner kinetochore structure.

PubMed

Tschernyschkow, Sergej; Herda, Sabine; Gruenert, Gerd; Döring, Volker; Görlich, Dennis; Hofmeister, Antje; Hoischen, Christian; Dittrich, Peter; Diekmann, Stephan; Ibrahim, Bashar

2013-09-01

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins. Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts. Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores. Copyright © 2013 Elsevier Ltd. All rights reserved.

Online Assistants in Children's Hypermedia Software

ERIC Educational Resources Information Center

Garcia, Penny Ann

2002-01-01

The classroom teacher's comfort and familiarity with computers and software influences student-computer use in the classroom. Teachers remain mired in repetitive introduction of basic software mechanics and rarely progress with students to advanced concepts or complex applications. An Online Assistant (OLA) was developed to accompany the…

Software Development Management: Empirical and Analytical Perspectives

ERIC Educational Resources Information Center

Kang, Keumseok

2011-01-01

Managing software development is a very complex activity because it must deal with people, organizations, technologies, and business processes. My dissertation consists of three studies that examine software development management from various perspectives. The first study empirically investigates the impacts of prior experience with similar…

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

PubMed

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.

Technical Reference Suite Addressing Challenges of Providing Assurance for Fault Management Architectural Design

NASA Technical Reports Server (NTRS)

Fitz, Rhonda; Whitman, Gerek

2016-01-01

Research into complexities of software systems Fault Management (FM) and how architectural design decisions affect safety, preservation of assets, and maintenance of desired system functionality has coalesced into a technical reference (TR) suite that advances the provision of safety and mission assurance. The NASA Independent Verification and Validation (IVV) Program, with Software Assurance Research Program support, extracted FM architectures across the IVV portfolio to evaluate robustness, assess visibility for validation and test, and define software assurance methods applied to the architectures and designs. This investigation spanned IVV projects with seven different primary developers, a wide range of sizes and complexities, and encompassed Deep Space Robotic, Human Spaceflight, and Earth Orbiter mission FM architectures. The initiative continues with an expansion of the TR suite to include Launch Vehicles, adding the benefit of investigating differences intrinsic to model-based FM architectures and insight into complexities of FM within an Agile software development environment, in order to improve awareness of how nontraditional processes affect FM architectural design and system health management.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

PubMed

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

Assurance of Complex Electronics. What Path Do We Take?

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Many of the methods used to develop software bare a close resemblance to Complex Electronics (CE) development. CE are now programmed to perform tasks that were previously handled in software, such as communication protocols. For instance, Field Programmable Gate Arrays (FPGAs) can have over a million logic gates while system-on-chip (SOC) devices can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of "software-like" bugs such as incorrect design, logic, and unexpected interactions within the logic is great. Since CE devices are obscuring the hardware/software boundary, we propose that mature software methodologies may be utilized with slight modifications to develop these devices. By using standardized S/W Engineering methods such as checklists, missing requirements and "bugs" can be detected earlier in the development cycle, thus creating a development process for CE that will be easily maintained and configurable based on the device used.

GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis.

PubMed

Gonzalez, Michael A; Lebrigio, Rafael F Acosta; Van Booven, Derek; Ulloa, Rick H; Powell, Eric; Speziani, Fiorella; Tekin, Mustafa; Schüle, Rebecca; Züchner, Stephan

2013-06-01

Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges, we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ∼1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 sec across ∼1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease. © 2013 Wiley Periodicals, Inc.

hEIDI: An Intuitive Application Tool To Organize and Treat Large-Scale Proteomics Data.

PubMed

Hesse, Anne-Marie; Dupierris, Véronique; Adam, Claire; Court, Magali; Barthe, Damien; Emadali, Anouk; Masselon, Christophe; Ferro, Myriam; Bruley, Christophe

2016-10-07

Advances in high-throughput proteomics have led to a rapid increase in the number, size, and complexity of the associated data sets. Managing and extracting reliable information from such large series of data sets require the use of dedicated software organized in a consistent pipeline to reduce, validate, exploit, and ultimately export data. The compilation of multiple mass-spectrometry-based identification and quantification results obtained in the context of a large-scale project represents a real challenge for developers of bioinformatics solutions. In response to this challenge, we developed a dedicated software suite called hEIDI to manage and combine both identifications and semiquantitative data related to multiple LC-MS/MS analyses. This paper describes how, through a user-friendly interface, hEIDI can be used to compile analyses and retrieve lists of nonredundant protein groups. Moreover, hEIDI allows direct comparison of series of analyses, on the basis of protein groups, while ensuring consistent protein inference and also computing spectral counts. hEIDI ensures that validated results are compliant with MIAPE guidelines as all information related to samples and results is stored in appropriate databases. Thanks to the database structure, validated results generated within hEIDI can be easily exported in the PRIDE XML format for subsequent publication. hEIDI can be downloaded from http://biodev.extra.cea.fr/docs/heidi .

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

NASA Astrophysics Data System (ADS)

Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William R.; Marty, Michael T.

2018-04-01

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. [Figure not available: see fulltext.

Virtual Immunology: Software for Teaching Basic Immunology

ERIC Educational Resources Information Center

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…

The Case for Open Source Software: The Interactional Discourse Lab

ERIC Educational Resources Information Center

Choi, Seongsook

2016-01-01

Computational techniques and software applications for the quantitative content analysis of texts are now well established, and many qualitative data software applications enable the manipulation of input variables and the visualization of complex relations between them via interactive and informative graphical interfaces. Although advances in…

A mass spectrometry proteomics data management platform.

PubMed

Sharma, Vagisha; Eng, Jimmy K; Maccoss, Michael J; Riffle, Michael

2012-09-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are "organically" distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/.

Nesting large-eddy simulations within mesoscale simulations for wind energy applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lundquist, J K; Mirocha, J D; Chow, F K

2008-09-08

With increasing demand for more accurate atmospheric simulations for wind turbine micrositing, for operational wind power forecasting, and for more reliable turbine design, simulations of atmospheric flow with resolution of tens of meters or higher are required. These time-dependent large-eddy simulations (LES), which resolve individual atmospheric eddies on length scales smaller than turbine blades and account for complex terrain, are possible with a range of commercial and open-source software, including the Weather Research and Forecasting (WRF) model. In addition to 'local' sources of turbulence within an LES domain, changing weather conditions outside the domain can also affect flow, suggesting thatmore » a mesoscale model provide boundary conditions to the large-eddy simulations. Nesting a large-eddy simulation within a mesoscale model requires nuanced representations of turbulence. Our group has improved the Weather and Research Forecasting model's (WRF) LES capability by implementing the Nonlinear Backscatter and Anisotropy (NBA) subfilter stress model following Kosovic (1997) and an explicit filtering and reconstruction technique to compute the Resolvable Subfilter-Scale (RSFS) stresses (following Chow et al, 2005). We have also implemented an immersed boundary method (IBM) in WRF to accommodate complex terrain. These new models improve WRF's LES capabilities over complex terrain and in stable atmospheric conditions. We demonstrate approaches to nesting LES within a mesoscale simulation for farms of wind turbines in hilly regions. Results are sensitive to the nesting method, indicating that care must be taken to provide appropriate boundary conditions, and to allow adequate spin-up of turbulence in the LES domain.« less

Creating an open environment software infrastructure

NASA Technical Reports Server (NTRS)

Jipping, Michael J.

1992-01-01

As the development of complex computer hardware accelerates at increasing rates, the ability of software to keep pace is essential. The development of software design tools, however, is falling behind the development of hardware for several reasons, the most prominent of which is the lack of a software infrastructure to provide an integrated environment for all parts of a software system. The research was undertaken to provide a basis for answering this problem by investigating the requirements of open environments.

Software safety

NASA Technical Reports Server (NTRS)

Leveson, Nancy

1987-01-01

Software safety and its relationship to other qualities are discussed. It is shown that standard reliability and fault tolerance techniques will not solve the safety problem for the present. A new attitude requires: looking at what you do NOT want software to do along with what you want it to do; and assuming things will go wrong. New procedures and changes to entire software development process are necessary: special software safety analysis techniques are needed; and design techniques, especially eliminating complexity, can be very helpful.

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Executable assertions and flight software

NASA Technical Reports Server (NTRS)

Mahmood, A.; Andrews, D. M.; Mccluskey, E. J.

1984-01-01

Executable assertions are used to test flight control software. The techniques used for testing flight software; however, are different from the techniques used to test other kinds of software. This is because of the redundant nature of flight software. An experimental setup for testing flight software using executable assertions is described. Techniques for writing and using executable assertions to test flight software are presented. The error detection capability of assertions is studied and many examples of assertions are given. The issues of placement and complexity of assertions and the language features to support efficient use of assertions are discussed.

Analysis of Software Systems for Specialized Computers,

DTIC Science & Technology

computer) with given computer hardware and software . The object of study is the software system of a computer, designed for solving a fixed complex of...purpose of the analysis is to find parameters that characterize the system and its elements during operation, i.e., when servicing the given requirement flow. (Author)

Assurance Evaluation for OSS Adoption in a Telco Context

NASA Astrophysics Data System (ADS)

Ardagna, Claudio A.; Banzi, Massimo; Damiani, Ernesto; El Ioini, Nabil; Frati, Fulvio

Software Assurance (SwA) is a complex concept that involves different stages of a software development process and may be defined differently depending on its focus, as for instance software quality, security, or dependability. In Computer Science, the term assurance is referred to all activities necessary to provide enough confidence that a software product will satisfy its users’ functional and non-functional requirements.

Conceptions of Software Development by Project Managers: A Study of Managing the Outsourced Development of Software Applications for United States Federal Government Agencies

ERIC Educational Resources Information Center

Eisen, Daniel

2013-01-01

This study explores how project managers, working for private federal IT contractors, experience and understand managing the development of software applications for U.S. federal government agencies. Very little is known about how they manage their projects in this challenging environment. Software development is a complex task and only grows in…

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE PAGES

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto; ...

2017-09-15

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

Time assignment system and its performance aboard the Hitomi satellite

NASA Astrophysics Data System (ADS)

Terada, Yukikatsu; Yamaguchi, Sunao; Sugimoto, Shigenobu; Inoue, Taku; Nakaya, Souhei; Murakami, Maika; Yabe, Seiya; Oshimizu, Kenya; Ogawa, Mina; Dotani, Tadayasu; Ishisaki, Yoshitaka; Mizushima, Kazuyo; Kominato, Takashi; Mine, Hiroaki; Hihara, Hiroki; Iwase, Kaori; Kouzu, Tomomi; Tashiro, Makoto S.; Natsukari, Chikara; Ozaki, Masanobu; Kokubun, Motohide; Takahashi, Tadayuki; Kawakami, Satoko; Kasahara, Masaru; Kumagai, Susumu; Angelini, Lorella; Witthoeft, Michael

2018-01-01

Fast timing capability in x-ray observation of astrophysical objects is one of the key properties for the ASTRO-H (Hitomi) mission. Absolute timing accuracies of 350 or 35 μs are required to achieve nominal scientific goals or to study fast variabilities of specific sources. The satellite carries a GPS receiver to obtain accurate time information, which is distributed from the central onboard computer through the large and complex SpaceWire network. The details of the time system on the hardware and software design are described. In the distribution of the time information, the propagation delays and jitters affect the timing accuracy. Six other items identified within the timing system will also contribute to absolute time error. These error items have been measured and checked on ground to ensure the time error budgets meet the mission requirements. The overall timing performance in combination with hardware performance, software algorithm, and the orbital determination accuracies, etc. under nominal conditions satisfies the mission requirements of 35 μs. This work demonstrates key points for space-use instruments in hardware and software designs and calibration measurements for fine timing accuracy on the order of microseconds for midsized satellites using the SpaceWire (IEEE1355) network.

Integrating manufacturing softwares for intelligent planning execution: a CIIMPLEX perspective

NASA Astrophysics Data System (ADS)

Chu, Bei Tseng B.; Tolone, William J.; Wilhelm, Robert G.; Hegedus, M.; Fesko, J.; Finin, T.; Peng, Yun; Jones, Chris H.; Long, Junshen; Matthews, Mike; Mayfield, J.; Shimp, J.; Su, S.

1997-01-01

Recent developments have made it possible to interoperate complex business applications at much lower costs. Application interoperation, along with business process re- engineering can result in significant savings by eliminating work created by disconnected business processes due to isolated business applications. However, we believe much greater productivity benefits can be achieved by facilitating timely decision-making, utilizing information from multiple enterprise perspectives. The CIIMPLEX enterprise integration architecture is designed to enable such productivity gains by helping people to carry out integrated enterprise scenarios. An enterprise scenario is triggered typically by some external event. The goal of an enterprise scenario is to make the right decisions considering the full context of the problem. Enterprise scenarios are difficult for people to carry out because of the interdependencies among various actions. One can easily be overwhelmed by the large amount of information. We propose the use of software agents to help gathering relevant information and present them in the appropriate context of an enterprise scenario. The CIIMPLEX enterprise integration architecture is based on the FAIME methodology for application interoperation and plug-and-play. It also explores the use of software agents in application plug-and- play.

ELSI: A unified software interface for Kohn-Sham electronic structure solvers

NASA Astrophysics Data System (ADS)

Yu, Victor Wen-zhe; Corsetti, Fabiano; García, Alberto; Huhn, William P.; Jacquelin, Mathias; Jia, Weile; Lange, Björn; Lin, Lin; Lu, Jianfeng; Mi, Wenhui; Seifitokaldani, Ali; Vázquez-Mayagoitia, Álvaro; Yang, Chao; Yang, Haizhao; Blum, Volker

2018-01-01

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.

SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

PubMed

Wang, Lin; Liu, Simin; Niu, Tianhua; Xu, Xin

2005-03-18

Single nucleotide polymorphisms (SNPs) provide an important tool in pinpointing susceptibility genes for complex diseases and in unveiling human molecular evolution. Selection and retrieval of an optimal SNP set from publicly available databases have emerged as the foremost bottlenecks in designing large-scale linkage disequilibrium studies, particularly in case-control settings. We describe the architectural structure and implementations of a novel software program, SNPHunter, which allows for both ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data, including physical position, function class, flanking sequences at user-defined lengths, and heterozygosity from NCBI dbSNP. The SNP data extracted from dbSNP via SNPHunter can be exported and saved in plain text format for further down-stream analyses. As an illustration, we applied SNPHunter for selecting SNPs for 10 major candidate genes for type 2 diabetes, including CAPN10, FABP4, IL6, NOS3, PPARG, TNF, UCP2, CRP, ESR1, and AR. SNPHunter constitutes an efficient and user-friendly tool for SNP screening, selection, and acquisition. The executable and user's manual are available at http://www.hsph.harvard.edu/ppg/software.htm

Calculus domains modelled using an original bool algebra based on polygons

NASA Astrophysics Data System (ADS)

Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

2016-08-01

Analytical and numerical computer based models require analytical definitions of the calculus domains. The paper presents a method to model a calculus domain based on a bool algebra which uses solid and hollow polygons. The general calculus relations of the geometrical characteristics that are widely used in mechanical engineering are tested using several shapes of the calculus domain in order to draw conclusions regarding the most effective methods to discretize the domain. The paper also tests the results of several CAD commercial software applications which are able to compute the geometrical characteristics, being drawn interesting conclusions. The tests were also targeting the accuracy of the results vs. the number of nodes on the curved boundary of the cross section. The study required the development of an original software consisting of more than 1700 computer code lines. In comparison with other calculus methods, the discretization using convex polygons is a simpler approach. Moreover, this method doesn't lead to large numbers as the spline approximation did, in that case being required special software packages in order to offer multiple, arbitrary precision. The knowledge resulted from this study may be used to develop complex computer based models in engineering.

Dypas: A dynamic payload scheduler for shuttle missions

NASA Technical Reports Server (NTRS)

Davis, Stephen

1988-01-01

Decision and analysis systems have had broad and very practical application areas in the human decision making process. These software systems range from the help sections in simple accounting packages, to the more complex computer configuration programs. Dypas is a decision and analysis system that aids prelaunch shutlle scheduling, and has added functionality to aid the rescheduling done in flight. Dypas is written in Common Lisp on a Symbolics Lisp machine. Dypas differs from other scheduling programs in that it can draw its knowledge from different rule bases and apply them to different rule interpretation schemes. The system has been coded with Flavors, an object oriented extension to Common Lisp on the Symbolics hardware. This allows implementation of objects (experiments) to better match the problem definition, and allows a more coherent solution space to be developed. Dypas was originally developed to test a programmer's aptitude toward Common Lisp and the Symbolics software environment. Since then the system has grown into a large software effort with several programmers and researchers thrown into the effort. Dypas is currently using two expert systems and three inferencing procedures to generate a many object schedule. The paper will review the abilities of Dypas and comment on its functionality.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data

PubMed Central

Li, Lingyun; Zhang, Fuming; Hu, Min; Ren, Fuji; Chi, Lianli; Linhardt, Robert J.

2016-01-01

Low molecular weight heparins are complex polycomponent drugs that have recently become amenable to top-down analysis using liquid chromatography-mass spectrometry. Even using open source deconvolution software, DeconTools, and automatic structural assignment software, GlycReSoft, the comparison of two or more low molecular weight heparins is extremely time-consuming, taking about a week for an expert analyst and provides no guarantee of accuracy. Efficient data processing tools are required to improve analysis. This study uses the programming language of Microsoft Excel™ Visual Basic for Applications to extend its standard functionality for macro functions and specific mathematical modules for mass spectrometric data processing. The program developed enables the comparison of top-down analytical glycomics data on two or more low molecular weight heparins. The current study describes a new program, GlycCompSoft, which has a low error rate with good time efficiency in the automatic processing of large data sets. The experimental results based on three lots of Lovenox®, Clexane® and three generic enoxaparin samples show that the run time of GlycCompSoft decreases from 11 to 2 seconds when the data processed decreases from 18000 to 1500 rows. PMID:27942011

On the recognition of complex structures: Computer software using artificial intelligence applied to pattern recognition

NASA Technical Reports Server (NTRS)

Yakimovsky, Y.

1974-01-01

An approach to simultaneous interpretation of objects in complex structures so as to maximize a combined utility function is presented. Results of the application of a computer software system to assign meaning to regions in a segmented image based on the principles described in this paper and on a special interactive sequential classification learning system, which is referenced, are demonstrated.

Computerized Dental Comparison: A Critical Review of Dental Coding and Ranking Algorithms Used in Victim Identification.

PubMed

Adams, Bradley J; Aschheim, Kenneth W

2016-01-01

Comparison of antemortem and postmortem dental records is a leading method of victim identification, especially for incidents involving a large number of decedents. This process may be expedited with computer software that provides a ranked list of best possible matches. This study provides a comparison of the most commonly used conventional coding and sorting algorithms used in the United States (WinID3) with a simplified coding format that utilizes an optimized sorting algorithm. The simplified system consists of seven basic codes and utilizes an optimized algorithm based largely on the percentage of matches. To perform this research, a large reference database of approximately 50,000 antemortem and postmortem records was created. For most disaster scenarios, the proposed simplified codes, paired with the optimized algorithm, performed better than WinID3 which uses more complex codes. The detailed coding system does show better performance with extremely large numbers of records and/or significant body fragmentation. © 2015 American Academy of Forensic Sciences.

Verification and Validation for Flight-Critical Systems (VVFCS)

NASA Technical Reports Server (NTRS)

Graves, Sharon S.; Jacobsen, Robert A.

2010-01-01

On March 31, 2009 a Request for Information (RFI) was issued by NASA s Aviation Safety Program to gather input on the subject of Verification and Validation (V & V) of Flight-Critical Systems. The responses were provided to NASA on or before April 24, 2009. The RFI asked for comments in three topic areas: Modeling and Validation of New Concepts for Vehicles and Operations; Verification of Complex Integrated and Distributed Systems; and Software Safety Assurance. There were a total of 34 responses to the RFI, representing a cross-section of academic (26%), small & large industry (47%) and government agency (27%).

Managing Analysis Models in the Design Process

NASA Technical Reports Server (NTRS)

Briggs, Clark

2006-01-01

Design of large, complex space systems depends on significant model-based support for exploration of the design space. Integrated models predict system performance in mission-relevant terms given design descriptions and multiple physics-based numerical models. Both the design activities and the modeling activities warrant explicit process definitions and active process management to protect the project from excessive risk. Software and systems engineering processes have been formalized and similar formal process activities are under development for design engineering and integrated modeling. JPL is establishing a modeling process to define development and application of such system-level models.

In-depth evaluation of software tools for data-independent acquisition based label-free quantification.

PubMed

Kuharev, Jörg; Navarro, Pedro; Distler, Ute; Jahn, Olaf; Tenzer, Stefan

2015-09-01

Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In order to benchmark the LFQ performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, Escherichia coli). This model dataset simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and downregulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on quantification results. Analysis of technical reproducibility revealed median coefficients of variation of reported protein abundances below 5% for MS(E) data for Progenesis and ISOQuant. Regarding accuracy of LFQ, evaluation with synapter and ISOQuant yielded superior results compared to Progenesis. In addition, we discuss reporting formats and user friendliness of the software packages. The data generated in this study have been deposited to the ProteomeXchange Consortium with identifier PXD001240 (http://proteomecentral.proteomexchange.org/dataset/PXD001240). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trusted Autonomy for Space Flight Systems

NASA Technical Reports Server (NTRS)

Freed, Michael; Bonasso, Pete; Ingham, Mitch; Kortenkamp, David; Perix, John

2005-01-01

NASA has long supported research on intelligent control technologies that could allow space systems to operate autonomously or with reduced human supervision. Proposed uses range from automated control of entire space vehicles to mobile robots that assist or substitute for astronauts to vehicle systems such as life support that interact with other systems in complex ways and require constant vigilance. The potential for pervasive use of such technology to extend the kinds of missions that are possible in practice is well understood, as is its potential to radically improve the robustness, safety and productivity of diverse mission systems. Despite its acknowledged potential, intelligent control capabilities are rarely used in space flight systems. Perhaps the most famous example of intelligent control on a spacecraft is the Remote Agent system flown on the Deep Space One mission (1998 - 2001). However, even in this case, the role of the intelligent control element, originally intended to have full control of the spacecraft for the duration of the mission, was reduced to having partial control for a two-week non-critical period. Even this level of mission acceptance was exceptional. In most cases, mission managers consider intelligent control systems an unacceptable source of risk and elect not to fly them. Overall, the technology is not trusted. From the standpoint of those who need to decide whether to incorporate this technology, lack of trust is easy to understand. Intelligent high-level control means allowing software io make decisions that are too complex for conventional software. The decision-making behavior of these systems is often hard to understand and inspect, and thus hard to evaluate. Moreover, such software is typically designed and implemented either as a research product or custom-built for a particular mission. In the former case, software quality is unlikely to be adequate for flight qualification and the functionality provided by the system is likely driven largely by the need to publish innovative work. In the latter case, the mission represents the first use of the system, a risky proposition even for relatively simple software.

Software ion scan functions in analysis of glycomic and lipidomic MS/MS datasets.

PubMed

Haramija, Marko

2018-03-01

Hardware ion scan functions unique to tandem mass spectrometry (MS/MS) mode of data acquisition, such as precursor ion scan (PIS) and neutral loss scan (NLS), are important for selective extraction of key structural data from complex MS/MS spectra. However, their software counterparts, software ion scan (SIS) functions, are still not regularly available. Software ion scan functions can be easily coded for additional functionalities, such as software multiple precursor ion scan, software no ion scan, and software variable ion scan functions. These are often necessary, since they allow more efficient analysis of complex MS/MS datasets, often encountered in glycomics and lipidomics. Software ion scan functions can be easily coded by using modern script languages and can be independent of instrument manufacturer. Here we demonstrate the utility of SIS functions on a medium-size glycomic MS/MS dataset. Knowledge of sample properties, as well as of diagnostic and conditional diagnostic ions crucial for data analysis, was needed. Based on the tables constructed with the output data from the SIS functions performed, a detailed analysis of a complex MS/MS glycomic dataset could be carried out in a quick, accurate, and efficient manner. Glycomic research is progressing slowly, and with respect to the MS experiments, one of the key obstacles for moving forward is the lack of appropriate bioinformatic tools necessary for fast analysis of glycomic MS/MS datasets. Adding novel SIS functionalities to the glycomic MS/MS toolbox has a potential to significantly speed up the glycomic data analysis process. Similar tools are useful for analysis of lipidomic MS/MS datasets as well, as will be discussed briefly. Copyright © 2017 John Wiley & Sons, Ltd.

A methodology for model-based development and automated verification of software for aerospace systems

NASA Astrophysics Data System (ADS)

Martin, L.; Schatalov, M.; Hagner, M.; Goltz, U.; Maibaum, O.

Today's software for aerospace systems typically is very complex. This is due to the increasing number of features as well as the high demand for safety, reliability, and quality. This complexity also leads to significant higher software development costs. To handle the software complexity, a structured development process is necessary. Additionally, compliance with relevant standards for quality assurance is a mandatory concern. To assure high software quality, techniques for verification are necessary. Besides traditional techniques like testing, automated verification techniques like model checking become more popular. The latter examine the whole state space and, consequently, result in a full test coverage. Nevertheless, despite the obvious advantages, this technique is rarely yet used for the development of aerospace systems. In this paper, we propose a tool-supported methodology for the development and formal verification of safety-critical software in the aerospace domain. The methodology relies on the V-Model and defines a comprehensive work flow for model-based software development as well as automated verification in compliance to the European standard series ECSS-E-ST-40C. Furthermore, our methodology supports the generation and deployment of code. For tool support we use the tool SCADE Suite (Esterel Technology), an integrated design environment that covers all the requirements for our methodology. The SCADE Suite is well established in avionics and defense, rail transportation, energy and heavy equipment industries. For evaluation purposes, we apply our approach to an up-to-date case study of the TET-1 satellite bus. In particular, the attitude and orbit control software is considered. The behavioral models for the subsystem are developed, formally verified, and optimized.

The State of Software for Evolutionary Biology.

PubMed

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-05-01

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.

Surface CHEMKIN (Version 4. 0): A Fortran package for analyzing heterogeneous chemical kinetics at a solid-surface---gas-phase interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coltrin, M.E.; Kee, R.J.; Rupley, F.M.

1991-07-01

Heterogeneous reaction at the interface between a solid surface and adjacent gas is central to many chemical processes. Our purpose for developing the software package SURFACE CHEMKIN was motivated by our need to understand the complex surface chemistry in chemical vapor deposition systems involving silicon, silicon nitride, and gallium arsenide. However, we have developed the approach and implemented the software in a general setting. Thus, we expect it will find use in such diverse applications as chemical vapor deposition, chemical etching, combustion of solids, and catalytic processes, and for a wide range of chemical systems. We believe that it providesmore » a powerful capability to help model, understand, and optimize important industrial and research chemical processes. The SURFACE CHEMKIN software is designed to work in conjunction with the CHEMKIN-2 software, which handles the chemical kinetics in the gas phase. It may also be used in conjunction with the Transport Property Package, which provides information about molecular diffusion. Thus, these three packages provide a foundation on which a user can build applications software to analyze gas-phase and heterogeneous chemistry in flowing systems. These packages should not be considered programs'' in the ordinary sense. That is, they are not designed to accept input, solve a particular problem, and report the answer. Instead, they are software tools intended to help a user work efficiently with large systems of chemical reactions and develop Fortran representations of systems of equations that define a particular problem. It is up the user to solve the problem and interpret the answer. 11 refs., 15 figs., 5 tabs.« less

Computational science: shifting the focus from tools to models

PubMed Central

Hinsen, Konrad

2014-01-01

Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication of big data sets or complex models. As a consequence, these crucial pieces of information no longer enter the scientific record. Moreover, they have become prisoners of scientific software: many models exist only as software implementations, and the data are often stored in proprietary formats defined by the software. In this article, I argue that this emphasis on software tools over models and data is detrimental to science in the long term, and I propose a means by which this can be reversed. PMID:25309728

The Simple Concurrent Online Processing System (SCOPS) - An open-source interface for remotely sensed data processing

NASA Astrophysics Data System (ADS)

Warren, M. A.; Goult, S.; Clewley, D.

2018-06-01

Advances in technology allow remotely sensed data to be acquired with increasingly higher spatial and spectral resolutions. These data may then be used to influence government decision making and solve a number of research and application driven questions. However, such large volumes of data can be difficult to handle on a single personal computer or on older machines with slower components. Often the software required to process data is varied and can be highly technical and too advanced for the novice user to fully understand. This paper describes an open-source tool, the Simple Concurrent Online Processing System (SCOPS), which forms part of an airborne hyperspectral data processing chain that allows users accessing the tool over a web interface to submit jobs and process data remotely. It is demonstrated using Natural Environment Research Council Airborne Research Facility (NERC-ARF) instruments together with other free- and open-source tools to take radiometrically corrected data from sensor geometry into geocorrected form and to generate simple or complex band ratio products. The final processed data products are acquired via an HTTP download. SCOPS can cut data processing times and introduce complex processing software to novice users by distributing jobs across a network using a simple to use web interface.

An ontology-based semantic configuration approach to constructing Data as a Service for enterprises

NASA Astrophysics Data System (ADS)

Cai, Hongming; Xie, Cheng; Jiang, Lihong; Fang, Lu; Huang, Chenxi

2016-03-01

To align business strategies with IT systems, enterprises should rapidly implement new applications based on existing information with complex associations to adapt to the continually changing external business environment. Thus, Data as a Service (DaaS) has become an enabling technology for enterprise through information integration and the configuration of existing distributed enterprise systems and heterogonous data sources. However, business modelling, system configuration and model alignment face challenges at the design and execution stages. To provide a comprehensive solution to facilitate data-centric application design in a highly complex and large-scale situation, a configurable ontology-based service integrated platform (COSIP) is proposed to support business modelling, system configuration and execution management. First, a meta-resource model is constructed and used to describe and encapsulate information resources by way of multi-view business modelling. Then, based on ontologies, three semantic configuration patterns, namely composite resource configuration, business scene configuration and runtime environment configuration, are designed to systematically connect business goals with executable applications. Finally, a software architecture based on model-view-controller (MVC) is provided and used to assemble components for software implementation. The result of the case study demonstrates that the proposed approach provides a flexible method of implementing data-centric applications.

BigDataScript: a scripting language for data pipelines.

PubMed

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. © The Author 2014. Published by Oxford University Press.

BigDataScript: a scripting language for data pipelines

PubMed Central

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. Contact: pablo.e.cingolani@gmail.com PMID:25189778

Commercial Literacy Software.

ERIC Educational Resources Information Center

Balajthy, Ernest

1997-01-01

Presents the first year's results of a continuing project to monitor the availability of software of relevance for literacy education purposes. Concludes there is an enormous amount of software available for use by teachers of reading and literacy--whereas drill-and-practice software is the largest category of software available, large numbers of…

Promoting linguistic complexity, greater message length and ease of engagement in email writing in people with aphasia: initial evidence from a study utilizing assistive writing software.

PubMed

Thiel, Lindsey; Sage, Karen; Conroy, Paul

2017-01-01

Improving email writing in people with aphasia could enhance their ability to communicate, promote interaction and reduce isolation. Spelling therapies have been effective in improving single-word writing. However, there has been limited evidence on how to achieve changes to everyday writing tasks such as email writing in people with aphasia. One potential area that has been largely unexplored in the literature is the potential use of assistive writing technologies, despite some initial evidence that assistive writing software use can lead to qualitative and quantitative improvements to spontaneous writing. This within-participants case series design study aimed to investigate the effects of using assistive writing software to improve email writing in participants with dysgraphia related to aphasia. Eight participants worked through a hierarchy of writing tasks of increasing complexity within broad topic areas that incorporate the spheres of writing need of the participants: writing for domestic needs, writing for social needs and writing for business/administrative needs. Through completing these tasks, participants had the opportunity to use the various functions of the software, such as predictive writing, word banks and text to speech. Therapy also included training and practice in basic computer and email skills to encourage increased independence. Outcome measures included email skills, keyboard skills, email writing and written picture description tasks, and a perception of disability assessment. Four of the eight participants showed statistically significant improvements to spelling accuracy within emails when using the software. At a group level there was a significant increase in word length with the software; while four participants showed noteworthy changes to the range of word classes used. Enhanced independence in email use and improvements in participants' perceptions of their writing skills were also noted. This study provided some initial evidence that assistive writing technologies can support people with aphasia in email writing across a range of important performance parameters. However, more research is needed to measure the effects of these technologies on the writing of people with aphasia, and to determine the optimal compensatory mechanisms for specific people given the linguistic-strategic resources they bring to the task of email writing. © 2016 Royal College of Speech and Language Therapists.

Demonstration of a Safety Analysis on a Complex System

NASA Technical Reports Server (NTRS)

Leveson, Nancy; Alfaro, Liliana; Alvarado, Christine; Brown, Molly; Hunt, Earl B.; Jaffe, Matt; Joslyn, Susan; Pinnell, Denise; Reese, Jon; Samarziya, Jeffrey;

Large area crop inventory experiment crop assessment subsystem software requirements document

NASA Technical Reports Server (NTRS)

1975-01-01

The functional data processing requirements are described for the Crop Assessment Subsystem of the Large Area Crop Inventory Experiment. These requirements are used as a guide for software development and implementation.

Salvus: A flexible open-source package for waveform modelling and inversion from laboratory to global scales

NASA Astrophysics Data System (ADS)

Afanasiev, M.; Boehm, C.; van Driel, M.; Krischer, L.; May, D.; Rietmann, M.; Fichtner, A.

2016-12-01

Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Based on a high order finite (spectral) element discretization, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and discuss some of the extensible design points.

Salvus: A flexible high-performance and open-source package for waveform modelling and inversion from laboratory to global scales

NASA Astrophysics Data System (ADS)

Afanasiev, Michael; Boehm, Christian; van Driel, Martin; Krischer, Lion; May, Dave; Rietmann, Max; Fichtner, Andreas

2017-04-01

Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Currently based on an abstract implementation of high order finite (spectral) elements, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. viscoelastic, coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ template mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and discuss some of the extensible design points.

freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

PubMed

Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

2015-01-01

Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

High-Dimensional Bayesian Geostatistics

PubMed Central

Banerjee, Sudipto

2017-01-01

With the growing capabilities of Geographic Information Systems (GIS) and user-friendly software, statisticians today routinely encounter geographically referenced data containing observations from a large number of spatial locations and time points. Over the last decade, hierarchical spatiotemporal process models have become widely deployed statistical tools for researchers to better understand the complex nature of spatial and temporal variability. However, fitting hierarchical spatiotemporal models often involves expensive matrix computations with complexity increasing in cubic order for the number of spatial locations and temporal points. This renders such models unfeasible for large data sets. This article offers a focused review of two methods for constructing well-defined highly scalable spatiotemporal stochastic processes. Both these processes can be used as “priors” for spatiotemporal random fields. The first approach constructs a low-rank process operating on a lower-dimensional subspace. The second approach constructs a Nearest-Neighbor Gaussian Process (NNGP) that ensures sparse precision matrices for its finite realizations. Both processes can be exploited as a scalable prior embedded within a rich hierarchical modeling framework to deliver full Bayesian inference. These approaches can be described as model-based solutions for big spatiotemporal datasets. The models ensure that the algorithmic complexity has ~ n floating point operations (flops), where n the number of spatial locations (per iteration). We compare these methods and provide some insight into their methodological underpinnings. PMID:29391920

High-Dimensional Bayesian Geostatistics.

PubMed

Banerjee, Sudipto

2017-06-01

With the growing capabilities of Geographic Information Systems (GIS) and user-friendly software, statisticians today routinely encounter geographically referenced data containing observations from a large number of spatial locations and time points. Over the last decade, hierarchical spatiotemporal process models have become widely deployed statistical tools for researchers to better understand the complex nature of spatial and temporal variability. However, fitting hierarchical spatiotemporal models often involves expensive matrix computations with complexity increasing in cubic order for the number of spatial locations and temporal points. This renders such models unfeasible for large data sets. This article offers a focused review of two methods for constructing well-defined highly scalable spatiotemporal stochastic processes. Both these processes can be used as "priors" for spatiotemporal random fields. The first approach constructs a low-rank process operating on a lower-dimensional subspace. The second approach constructs a Nearest-Neighbor Gaussian Process (NNGP) that ensures sparse precision matrices for its finite realizations. Both processes can be exploited as a scalable prior embedded within a rich hierarchical modeling framework to deliver full Bayesian inference. These approaches can be described as model-based solutions for big spatiotemporal datasets. The models ensure that the algorithmic complexity has ~ n floating point operations (flops), where n the number of spatial locations (per iteration). We compare these methods and provide some insight into their methodological underpinnings.

Property-Based Software Engineering Measurement

NASA Technical Reports Server (NTRS)

Briand, Lionel; Morasca, Sandro; Basili, Victor R.

1995-01-01

Little theory exists in the field of software system measurement. Concepts such as complexity, coupling, cohesion or even size are very often subject to interpretation and appear to have inconsistent definitions in the literature. As a consequence, there is little guidance provided to the analyst attempting to define proper measures for specific problems. Many controversies in the literature are simply misunderstandings and stem from the fact that some people talk about different measurement concepts under the same label (complexity is the most common case). There is a need to define unambiguously the most important measurement concepts used in the measurement of software products. One way of doing so is to define precisely what mathematical properties characterize these concepts regardless of the specific software artifacts to which these concepts are applied. Such a mathematical framework could generate a consensus in the software engineering community and provide a means for better communication among researchers, better guidelines for analysis, and better evaluation methods for commercial static analyzers for practitioners. In this paper, we propose a mathematical framework which is generic, because it is not specific to any particular software artifact, and rigorous, because it is based on precise mathematical concepts. This framework defines several important measurement concepts (size, length, complexity, cohesion, coupling). It is not intended to be complete or fully objective; other frameworks could have been proposed and different choices could have been made. However, we believe that the formalism and properties we introduce are convenient and intuitive. In addition, we have reviewed the literature on this subject and compared it with our work. This framework contributes constructively to a firmer theoretical ground of software measurement.

Property-Based Software Engineering Measurement

NASA Technical Reports Server (NTRS)

Briand, Lionel C.; Morasca, Sandro; Basili, Victor R.

1997-01-01

Little theory exists in the field of software system measurement. Concepts such as complexity, coupling, cohesion or even size are very often subject to interpretation and appear to have inconsistent definitions in the literature. As a consequence, there is little guidance provided to the analyst attempting to define proper measures for specific problems. Many controversies in the literature are simply misunderstandings and stem from the fact that some people talk about different measurement concepts under the same label (complexity is the most common case). There is a need to define unambiguously the most important measurement concepts used in the measurement of software products. One way of doing so is to define precisely what mathematical properties characterize these concepts, regardless of the specific software artifacts to which these concepts are applied. Such a mathematical framework could generate a consensus in the software engineering community and provide a means for better communication among researchers, better guidelines for analysts, and better evaluation methods for commercial static analyzers for practitioners. In this paper, we propose a mathematical framework which is generic, because it is not specific to any particular software artifact and rigorous, because it is based on precise mathematical concepts. We use this framework to propose definitions of several important measurement concepts (size, length, complexity, cohesion, coupling). It does not intend to be complete or fully objective; other frameworks could have been proposed and different choices could have been made. However, we believe that the formalisms and properties we introduce are convenient and intuitive. This framework contributes constructively to a firmer theoretical ground of software measurement.

Model Transformation for a System of Systems Dependability Safety Case

NASA Technical Reports Server (NTRS)

Murphy, Judy; Driskell, Stephen B.

2010-01-01

Software plays an increasingly larger role in all aspects of NASA's science missions. This has been extended to the identification, management and control of faults which affect safety-critical functions and by default, the overall success of the mission. Traditionally, the analysis of fault identification, management and control are hardware based. Due to the increasing complexity of system, there has been a corresponding increase in the complexity in fault management software. The NASA Independent Validation & Verification (IV&V) program is creating processes and procedures to identify, and incorporate safety-critical software requirements along with corresponding software faults so that potential hazards may be mitigated. This Specific to Generic ... A Case for Reuse paper describes the phases of a dependability and safety study which identifies a new, process to create a foundation for reusable assets. These assets support the identification and management of specific software faults and, their transformation from specific to generic software faults. This approach also has applications to other systems outside of the NASA environment. This paper addresses how a mission specific dependability and safety case is being transformed to a generic dependability and safety case which can be reused for any type of space mission with an emphasis on software fault conditions.

Return on Investment (ROI) Framework Case Study: CTH.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corro, Janna L.

CTH is a Eulerian code developed at Sandia National Laboratories capable of modeling the hydrodynamic response of explosives, liquids, gases, and solids. The code solves complex multi-dimensional problems characterized by large deformations and strong shocks that are composed of various material configurations. CTH includes models for material strength, fracture, porosity, and high explosive detonation and initiation. The code is an acronym for a complex series of names relating to its origin. A full explanation can be seen in Appendix A. The software breaks penetration simulations into millions of grid-like “cells”. As a modeled projectile impacts and penetrates a target, progressivelymore » smaller blocks of cells are placed around the projectile, which show in detail deformations and breakups. Additionally, the code is uniquely suited to modeling blunt impact and blast loading leading to human body injury.« less

A Parallel Rendering Algorithm for MIMD Architectures

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.; Orloff, Tobias

1991-01-01

Applications such as animation and scientific visualization demand high performance rendering of complex three dimensional scenes. To deliver the necessary rendering rates, highly parallel hardware architectures are required. The challenge is then to design algorithms and software which effectively use the hardware parallelism. A rendering algorithm targeted to distributed memory MIMD architectures is described. For maximum performance, the algorithm exploits both object-level and pixel-level parallelism. The behavior of the algorithm is examined both analytically and experimentally. Its performance for large numbers of processors is found to be limited primarily by communication overheads. An experimental implementation for the Intel iPSC/860 shows increasing performance from 1 to 128 processors across a wide range of scene complexities. It is shown that minimal modifications to the algorithm will adapt it for use on shared memory architectures as well.

Context sensitivity and ambiguity in component-based systems design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bespalko, S.J.; Sindt, A.

1997-10-01

Designers of components-based, real-time systems need to guarantee to correctness of soft-ware and its output. Complexity of a system, and thus the propensity for error, is best characterized by the number of states a component can encounter. In many cases, large numbers of states arise where the processing is highly dependent on context. In these cases, states are often missed, leading to errors. The following are proposals for compactly specifying system states which allow the factoring of complex components into a control module and a semantic processing module. Further, the need for methods that allow for the explicit representation ofmore » ambiguity and uncertainty in the design of components is discussed. Presented herein are examples of real-world problems which are highly context-sensitive or are inherently ambiguous.« less

Reengineering observatory operations for the time domain

NASA Astrophysics Data System (ADS)

Seaman, Robert L.; Vestrand, W. T.; Hessman, Frederic V.

2014-07-01

Observatories are complex scientific and technical institutions serving diverse users and purposes. Their telescopes, instruments, software, and human resources engage in interwoven workflows over a broad range of timescales. These workflows have been tuned to be responsive to concepts of observatory operations that were applicable when various assets were commissioned, years or decades in the past. The astronomical community is entering an era of rapid change increasingly characterized by large time domain surveys, robotic telescopes and automated infrastructures, and - most significantly - of operating modes and scientific consortia that span our individual facilities, joining them into complex network entities. Observatories must adapt and numerous initiatives are in progress that focus on redesigning individual components out of the astronomical toolkit. New instrumentation is both more capable and more complex than ever, and even simple instruments may have powerful observation scripting capabilities. Remote and queue observing modes are now widespread. Data archives are becoming ubiquitous. Virtual observatory standards and protocols and astroinformatics data-mining techniques layered on these are areas of active development. Indeed, new large-aperture ground-based telescopes may be as expensive as space missions and have similarly formal project management processes and large data management requirements. This piecewise approach is not enough. Whatever challenges of funding or politics facing the national and international astronomical communities it will be more efficient - scientifically as well as in the usual figures of merit of cost, schedule, performance, and risks - to explicitly address the systems engineering of the astronomical community as a whole.

System for decision analysis support on complex waste management issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shropshire, D.E.

1997-10-01

A software system called the Waste Flow Analysis has been developed and applied to complex environmental management processes for the United States Department of Energy (US DOE). The system can evaluate proposed methods of waste retrieval, treatment, storage, transportation, and disposal. Analysts can evaluate various scenarios to see the impacts to waste slows and schedules, costs, and health and safety risks. Decision analysis capabilities have been integrated into the system to help identify preferred alternatives based on a specific objectives may be to maximize the waste moved to final disposition during a given time period, minimize health risks, minimize costs,more » or combinations of objectives. The decision analysis capabilities can support evaluation of large and complex problems rapidly, and under conditions of variable uncertainty. The system is being used to evaluate environmental management strategies to safely disposition wastes in the next ten years and reduce the environmental legacy resulting from nuclear material production over the past forty years.« less

An Agile Constructionist Mentoring Methodology for Software Projects in the High School

ERIC Educational Resources Information Center

Meerbaum-Salant, Orni; Hazzan, Orit

2010-01-01

This article describes the construction process and evaluation of the Agile Constructionist Mentoring Methodology (ACMM), a mentoring method for guiding software development projects in the high school. The need for such a methodology has arisen due to the complexity of mentoring software project development in the high school. We introduce the…

Novice and Experienced Instructional Software Developers: Effects on Materials Created with Instructional Software Templates

ERIC Educational Resources Information Center

Boot, Eddy W.; van Merrienboer, Jeroen J. G.; Veerman, Arja L.

2007-01-01

The development of instructional software is a complex process, posing high demands to the technical and didactical expertise of developers. Domain specialists rather than professional developers are often responsible for it, but authoring tools with pre-structured templates claim to compensate for this limited experience. This study compares…

Enhancing Architecture-Implementation Conformance with Change Management and Support for Behavioral Mapping

ERIC Educational Resources Information Center

Zheng, Yongjie

2012-01-01

Software architecture plays an increasingly important role in complex software development. Its further application, however, is challenged by the fact that software architecture, over time, is often found not conformant to its implementation. This is usually caused by frequent development changes made to both artifacts. Against this background,…

MATTS- A Step Towards Model Based Testing

NASA Astrophysics Data System (ADS)

Herpel, H.-J.; Willich, G.; Li, J.; Xie, J.; Johansen, B.; Kvinnesland, K.; Krueger, S.; Barrios, P.

2016-08-01

In this paper we describe a Model Based approach to testing of on-board software and compare it with traditional validation strategy currently applied to satellite software. The major problems that software engineering will face over at least the next two decades are increasing application complexity driven by the need for autonomy and serious application robustness. In other words, how do we actually get to declare success when trying to build applications one or two orders of magnitude more complex than today's applications. To solve the problems addressed above the software engineering process has to be improved at least for two aspects: 1) Software design and 2) Software testing. The software design process has to evolve towards model-based approaches with extensive use of code generators. Today, testing is an essential, but time and resource consuming activity in the software development process. Generating a short, but effective test suite usually requires a lot of manual work and expert knowledge. In a model-based process, among other subtasks, test construction and test execution can also be partially automated. The basic idea behind the presented study was to start from a formal model (e.g. State Machines), generate abstract test cases which are then converted to concrete executable test cases (input and expected output pairs). The generated concrete test cases were applied to an on-board software. Results were collected and evaluated wrt. applicability, cost-efficiency, effectiveness at fault finding, and scalability.

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.

PubMed

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.

Large Scale Software Building with CMake in ATLAS

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The offline software of the ATLAS experiment at the Large Hadron Collider (LHC) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector’s trigger system to select LHC collision events during data taking. The ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows, many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications also require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the above mentioned software packages. This also makes it possible to develop and test new and modified packages on top of existing releases. The system also allows one to detect and execute partial rebuilds of the release based on single package changes. The build system makes use of CPack for building RPM packages out of the software releases, and CTest for running unit and integration tests. We report on the migration and integration of the ATLAS software to CMake and show working examples of this large scale project in production.

Challenges and Demands on Automated Software Revision

NASA Technical Reports Server (NTRS)

Bonakdarpour, Borzoo; Kulkarni, Sandeep S.

2008-01-01

In the past three decades, automated program verification has undoubtedly been one of the most successful contributions of formal methods to software development. However, when verification of a program against a logical specification discovers bugs in the program, manual manipulation of the program is needed in order to repair it. Thus, in the face of existence of numerous unverified and un- certified legacy software in virtually any organization, tools that enable engineers to automatically verify and subsequently fix existing programs are highly desirable. In addition, since requirements of software systems often evolve during the software life cycle, the issue of incomplete specification has become a customary fact in many design and development teams. Thus, automated techniques that revise existing programs according to new specifications are of great assistance to designers, developers, and maintenance engineers. As a result, incorporating program synthesis techniques where an algorithm generates a program, that is correct-by-construction, seems to be a necessity. The notion of manual program repair described above turns out to be even more complex when programs are integrated with large collections of sensors and actuators in hostile physical environments in the so-called cyber-physical systems. When such systems are safety/mission- critical (e.g., in avionics systems), it is essential that the system reacts to physical events such as faults, delays, signals, attacks, etc, so that the system specification is not violated. In fact, since it is impossible to anticipate all possible such physical events at design time, it is highly desirable to have automated techniques that revise programs with respect to newly identified physical events according to the system specification.

Bayesian Software Health Management for Aircraft Guidance, Navigation, and Control

NASA Technical Reports Server (NTRS)

Schumann, Johann; Mbaya, Timmy; Menghoel, Ole

2011-01-01

Modern aircraft, both piloted fly-by-wire commercial aircraft as well as UAVs, more and more depend on highly complex safety critical software systems with many sensors and computer-controlled actuators. Despite careful design and V&V of the software, severe incidents have happened due to malfunctioning software. In this paper, we discuss the use of Bayesian networks (BNs) to monitor the health of the on-board software and sensor system, and to perform advanced on-board diagnostic reasoning. We will focus on the approach to develop reliable and robust health models for the combined software and sensor systems.

Data Integration: Charting a Path Forward to 2035

DTIC Science & Technology

2011-02-14

New York, NY: Gotham Books, 2004. Seligman , Len. Mitre Corporation, e-mail interview, 6 Dec 2010. Singer, P.W. Wired for War: The Robotics...articles.aspx (accessed 4 Dec 2010). Ultra-Large-Scale Systems: The Software Challenge of the Future. Study lead Linda Northrup. Pittsburgh, PA: Carnegie...Virtualization?‖ 1. 41 Ultra-Large-Scale Systems: The Software Challenge of the Future. Study lead Linda Northrup. Pittsburgh, PA: Carnegie Mellon Software

Performance testing of LiDAR exploitation software

NASA Astrophysics Data System (ADS)

Varela-González, M.; González-Jorge, H.; Riveiro, B.; Arias, P.

2013-04-01

Mobile LiDAR systems are being used widely in recent years for many applications in the field of geoscience. One of most important limitations of this technology is the large computational requirements involved in data processing. Several software solutions for data processing are available in the market, but users are often unknown about the methodologies to verify their performance accurately. In this work a methodology for LiDAR software performance testing is presented and six different suites are studied: QT Modeler, AutoCAD Civil 3D, Mars 7, Fledermaus, Carlson and TopoDOT (all of them in x64). Results depict as QTModeler, TopoDOT and AutoCAD Civil 3D allow the loading of large datasets, while Fledermaus, Mars7 and Carlson do not achieve these powerful performance. AutoCAD Civil 3D needs large loading time in comparison with the most powerful softwares such as QTModeler and TopoDOT. Carlson suite depicts the poorest results among all the softwares under study, where point clouds larger than 5 million points cannot be loaded and loading time is very large in comparison with the other suites even for the smaller datasets. AutoCAD Civil 3D, Carlson and TopoDOT show more threads than other softwares like QTModeler, Mars7 and Fledermaus.

Massively parallelized Monte Carlo software to calculate the light propagation in arbitrarily shaped 3D turbid media

NASA Astrophysics Data System (ADS)

Zoller, Christian; Hohmann, Ansgar; Ertl, Thomas; Kienle, Alwin

2017-07-01

The Monte Carlo method is often referred as the gold standard to calculate the light propagation in turbid media [1]. Especially for complex shaped geometries where no analytical solutions are available the Monte Carlo method becomes very important [1, 2]. In this work a Monte Carlo software is presented, to simulate the light propagation in complex shaped geometries. To improve the simulation time the code is based on OpenCL such that graphics cards can be used as well as other computing devices. Within the software an illumination concept is presented to realize easily all kinds of light sources, like spatial frequency domain (SFD), optical fibers or Gaussian beam profiles. Moreover different objects, which are not connected to each other, can be considered simultaneously, without any additional preprocessing. This Monte Carlo software can be used for many applications. In this work the transmission spectrum of a tooth and the color reconstruction of a virtual object are shown, using results from the Monte Carlo software.

Ethical education in software engineering: responsibility in the production of complex systems.

PubMed

Génova, Gonzalo; González, M Rosario; Fraga, Anabel

2007-12-01

Among the various contemporary schools of moral thinking, consequence-based ethics, as opposed to rule-based, seems to have a good acceptance among professionals such as software engineers. But naïve consequentialism is intellectually too weak to serve as a practical guide in the profession. Besides, the complexity of software systems makes it very hard to know in advance the consequences that will derive from professional activities in the production of software. Therefore, following the spirit of well-known codes of ethics such as the ACM/IEEE's, we advocate for a more solid position in the ethical education of software engineers, which we call 'moderate deontologism', that takes into account both rules and consequences to assess the goodness of actions, and at the same time pays an adequate consideration to the absolute values of human dignity. In order to educate responsible professionals, however, this position should be complemented with a pedagogical approach to virtue ethics.