Real-time computing platform for spiking neurons (RT-spike).

PubMed

Ros, Eduardo; Ortigosa, Eva M; Agís, Rodrigo; Carrillo, Richard; Arnold, Michael

2006-07-01

A computing platform is described for simulating arbitrary networks of spiking neurons in real time. A hybrid computing scheme is adopted that uses both software and hardware components to manage the tradeoff between flexibility and computational power; the neuron model is implemented in hardware and the network model and the learning are implemented in software. The incremental transition of the software components into hardware is supported. We focus on a spike response model (SRM) for a neuron where the synapses are modeled as input-driven conductances. The temporal dynamics of the synaptic integration process are modeled with a synaptic time constant that results in a gradual injection of charge. This type of model is computationally expensive and is not easily amenable to existing software-based event-driven approaches. As an alternative we have designed an efficient time-based computing architecture in hardware, where the different stages of the neuron model are processed in parallel. Further improvements occur by computing multiple neurons in parallel using multiple processing units. This design is tested using reconfigurable hardware and its scalability and performance evaluated. Our overall goal is to investigate biologically realistic models for the real-time control of robots operating within closed action-perception loops, and so we evaluate the performance of the system on simulating a model of the cerebellum where the emulation of the temporal dynamics of the synaptic integration process is important.

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

NASA Technical Reports Server (NTRS)

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

PREMER: a Tool to Infer Biological Networks.

PubMed

Villaverde, Alejandro F; Becker, Kolja; Banga, Julio R

2017-10-04

Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems. The computational cost of such calculations can be alleviated by the use of compiled programs and parallelization. To this end we have developed PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction), a software toolbox that can run in parallel and sequential environments. It uses information theoretic criteria to recover network topology and determine the strength and causality of interactions, and allows incorporating prior knowledge, imputing missing data, and correcting outliers. PREMER is a free, open source software tool that does not require any commercial software. Its core algorithms are programmed in FORTRAN 90 and implement OpenMP directives. It has user interfaces in Python and MATLAB/Octave, and runs on Windows, Linux and OSX (https://sites.google.com/site/premertoolbox/).

CrossTalk. The Journal of Defense Software Engineering. Volume 23, Number 6, Nov/Dec 2010

DTIC Science & Technology

2010-11-01

Model of archi- tectural design. It guides developers to apply effort to their software architecture commensurate with the risks faced by...Driven Model is the promotion of risk to prominence. It is possible to apply the Risk-Driven Model to essentially any software development process...succeed without any planned architecture work, while many high-risk projects would fail without it . The Risk-Driven Model walks a middle path

Consistent Evolution of Software Artifacts and Non-Functional Models

DTIC Science & Technology

2014-11-14

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

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

ERIC Educational Resources Information Center

Tekinerdogan, Bedir

2011-01-01

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

The Knowledge-Based Software Assistant: Beyond CASE

NASA Technical Reports Server (NTRS)

Carozzoni, Joseph A.

1993-01-01

This paper will outline the similarities and differences between two paradigms of software development. Both support the whole software life cycle and provide automation for most of the software development process, but have different approaches. The CASE approach is based on a set of tools linked by a central data repository. This tool-based approach is data driven and views software development as a series of sequential steps, each resulting in a product. The Knowledge-Based Software Assistant (KBSA) approach, a radical departure from existing software development practices, is knowledge driven and centers around a formalized software development process. KBSA views software development as an incremental, iterative, and evolutionary process with development occurring at the specification level.

Simulation and animation of sensor-driven robots.

PubMed

Chen, C; Trivedi, M M; Bidlack, C R

1994-10-01

Most simulation and animation systems utilized in robotics are concerned with simulation of the robot and its environment without simulation of sensors. These systems have difficulty in handling robots that utilize sensory feedback in their operation. In this paper, a new design of an environment for simulation, animation, and visualization of sensor-driven robots is presented. As sensor technology advances, increasing numbers of robots are equipped with various types of sophisticated sensors. The main goal of creating the visualization environment is to aid the automatic robot programming and off-line programming capabilities of sensor-driven robots. The software system will help the users visualize the motion and reaction of the sensor-driven robot under their control program. Therefore, the efficiency of the software development is increased, the reliability of the software and the operation safety of the robot are ensured, and the cost of new software development is reduced. Conventional computer-graphics-based robot simulation and animation software packages lack of capabilities for robot sensing simulation. This paper describes a system designed to overcome this deficiency.

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.

PubMed

Lun, Aaron T L; Smyth, Gordon K

2015-08-19

Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.

Test-driven programming

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2013-12-01

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

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

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

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.

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

Simulation and animation of sensor-driven robots

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

Chen, C.; Trivedi, M.M.; Bidlack, C.R.

1994-10-01

Most simulation and animation systems utilized in robotics are concerned with simulation of the robot and its environment without simulation of sensors. These systems have difficulty in handling robots that utilize sensory feedback in their operation. In this paper, a new design of an environment for simulation, animation, and visualization of sensor-driven robots is presented. As sensor technology advances, increasing numbers of robots are equipped with various types of sophisticated sensors. The main goal of creating the visualization environment is to aide the automatic robot programming and off-line programming capabilities of sensor-driven robots. The software system will help the usersmore » visualize the motion and reaction of the sensor-driven robot under their control program. Therefore, the efficiency of the software development is increased, the reliability of the software and the operation safety of the robot are ensured, and the cost of new software development is reduced. Conventional computer-graphics-based robot simulation and animation software packages lack of capabilities for robot sensing simulation. This paper describes a system designed to overcome this deficiency.« less

LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

PubMed Central

Clasquin, Michelle F.; Melamud, Eugene; Rabinowitz, Joshua D.

2014-01-01

MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis. PMID:22389014

LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.

PubMed

Clasquin, Michelle F; Melamud, Eugene; Rabinowitz, Joshua D

2012-03-01

MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis.

Improving Collaboration by Standardization Efforts in Systems Biology

PubMed Central

Dräger, Andreas; Palsson, Bernhard Ø.

2014-01-01

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

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

PubMed Central

2011-01-01

Background Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integration and data driven decision-making. Recent advancements in distributed multi-relational directed graphs, implemented in the form of the Semantic Web make it possible to deal with complicated heterogeneous data in new and interesting ways. Results This paper presents a new approach, scenario driven data modelling (SDDM), that integrates multi-relational directed graphs with data streams. SDDM can be applied to virtually any data integration challenge with widely divergent types of data and data streams. In this work, we explored integrating genetics data with reports from traditional media. SDDM was applied to the New Delhi metallo-beta-lactamase gene (NDM-1), an emerging global health threat. The SDDM process constructed a scenario, created a RDF multi-relational directed graph that linked diverse types of data to the Semantic Web, implemented RDF conversion tools (RDFizers) to bring content into the Sematic Web, identified data streams and analytical routines to analyse those streams, and identified user requirements and graph traversals to meet end-user requirements. Conclusions We provided an example where SDDM was applied to a complex data integration challenge. The process created a model of the emerging NDM-1 health threat, identified and filled gaps in that model, and constructed reliable software that monitored data streams based on the scenario derived multi-relational directed graph. The SDDM process significantly reduced the software requirements phase by letting the scenario and resulting multi-relational directed graph define what is possible and then set the scope of the user requirements. Approaches like SDDM will be critical to the future of data intensive, data-driven science because they automate the process of converting massive data streams into usable knowledge. PMID:22165854

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

ERIC Educational Resources Information Center

de Hoog, Robert; And Others

1994-01-01

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

EcoliWiki: a wiki-based community resource for Escherichia coli

PubMed Central

McIntosh, Brenley K.; Renfro, Daniel P.; Knapp, Gwendowlyn S.; Lairikyengbam, Chanchala R.; Liles, Nathan M.; Niu, Lili; Supak, Amanda M.; Venkatraman, Anand; Zweifel, Adrienne E.; Siegele, Deborah A.; Hu, James C.

2012-01-01

EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates information on laboratory strains of Escherichia coli, its phages, plasmids and mobile genetic elements. As one of the early adopters of the wiki approach to model organism databases, EcoliWiki was designed to not only facilitate community-driven sharing of biological knowledge about E. coli as a model organism, but also to be interoperable with other data resources. EcoliWiki content currently covers genes from five laboratory E. coli strains, 21 bacteriophage genomes, F plasmid and eight transposons. EcoliWiki integrates the Mediawiki wiki platform with other open-source software tools and in-house software development to extend how wikis can be used for model organism databases. EcoliWiki can be accessed online at http://ecoliwiki.net. PMID:22064863

A Web interface generator for molecular biology programs in Unix.

PubMed

Letondal, C

2001-01-01

Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration. The program has been used for three years by about 15000 users throughout the world; it has recently been installed on other sites and evaluated as a standard user interface for EMBOSS programs.

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

NASA Astrophysics Data System (ADS)

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

2005-09-01

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

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

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

ERIC Educational Resources Information Center

Cabot, Jordi; Tisi, Massimo

2011-01-01

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

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

PubMed

Mungall, Christopher J; Emmert, David B

2007-07-01

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

UWB Tracking Software Development

NASA Technical Reports Server (NTRS)

Gross, Julia; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dusl, John; Ni, Jianjun; Rafford, Melinda

2006-01-01

An Ultra-Wideband (UWB) two-cluster Angle of Arrival (AOA) tracking prototype system is currently being developed and tested at NASA Johnson Space Center for space exploration applications. This talk discusses the software development efforts for this UWB two-cluster AOA tracking system. The role the software plays in this system is to take waveform data from two UWB radio receivers as an input, feed this input into an AOA tracking algorithm, and generate the target position as an output. The architecture of the software (Input/Output Interface and Algorithm Core) will be introduced in this talk. The development of this software has three phases. In Phase I, the software is mostly Matlab driven and calls C++ socket functions to provide the communication links to the radios. This is beneficial in the early stage when it is necessary to frequently test changes in the algorithm. Phase II of the development is to have the software mostly C++ driven and call a Matlab function for the AOA tracking algorithm. This is beneficial in order to send the tracking results to other systems and also to improve the tracking update rate of the system. The third phase is part of future work and is to have the software completely C++ driven with a graphics user interface. This software design enables the fine resolution tracking of the UWB two-cluster AOA tracking system.

The application of domain-driven design in NMS

NASA Astrophysics Data System (ADS)

Zhang, Jinsong; Chen, Yan; Qin, Shengjun

2011-12-01

In the traditional design approach of data-model-driven, system analysis and design phases are often separated which makes the demand information can not be expressed explicitly. The method is also easy to lead developer to the process-oriented programming, making codes between the modules or between hierarchies disordered. So it is hard to meet requirement of system scalability. The paper proposes a software hiberarchy based on rich domain model according to domain-driven design named FHRDM, then the Webwork + Spring + Hibernate (WSH) framework is determined. Domain-driven design aims to construct a domain model which not only meets the demand of the field where the software exists but also meets the need of software development. In this way, problems in Navigational Maritime System (NMS) development like big system business volumes, difficulty of requirement elicitation, high development costs and long development cycle can be resolved successfully.

Academic Testing and Grading with Spreadsheet Software.

ERIC Educational Resources Information Center

Ho, James K.

1987-01-01

Explains how spreadsheet software can be used in the design and grading of academic tests and in assigning grades. Macro programs and menu-driven software are highlighted and an example using IBM PCs and Lotus 1-2-3 software is given. (Author/LRW)

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

PubMed

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

2017-08-15

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

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

PubMed Central

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

2017-01-01

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

A composite computational model of liver glucose homeostasis. I. Building the composite model.

PubMed

Hetherington, J; Sumner, T; Seymour, R M; Li, L; Rey, M Varela; Yamaji, S; Saffrey, P; Margoninski, O; Bogle, I D L; Finkelstein, A; Warner, A

2012-04-07

A computational model of the glucagon/insulin-driven liver glucohomeostasis function, focusing on the buffering of glucose into glycogen, has been developed. The model exemplifies an 'engineering' approach to modelling in systems biology, and was produced by linking together seven component models of separate aspects of the physiology. The component models use a variety of modelling paradigms and degrees of simplification. Model parameters were determined by an iterative hybrid of fitting to high-scale physiological data, and determination from small-scale in vitro experiments or molecular biological techniques. The component models were not originally designed for inclusion within such a composite model, but were integrated, with modification, using our published modelling software and computational frameworks. This approach facilitates the development of large and complex composite models, although, inevitably, some compromises must be made when composing the individual models. Composite models of this form have not previously been demonstrated.

RE-PLAN: An Extensible Software Architecture to Facilitate Disaster Response Planning

PubMed Central

O’Neill, Martin; Mikler, Armin R.; Indrakanti, Saratchandra; Tiwari, Chetan; Jimenez, Tamara

2014-01-01

Computational tools are needed to make data-driven disaster mitigation planning accessible to planners and policymakers without the need for programming or GIS expertise. To address this problem, we have created modules to facilitate quantitative analyses pertinent to a variety of different disaster scenarios. These modules, which comprise the REsponse PLan ANalyzer (RE-PLAN) framework, may be used to create tools for specific disaster scenarios that allow planners to harness large amounts of disparate data and execute computational models through a point-and-click interface. Bio-E, a user-friendly tool built using this framework, was designed to develop and analyze the feasibility of ad hoc clinics for treating populations following a biological emergency event. In this article, the design and implementation of the RE-PLAN framework are described, and the functionality of the modules used in the Bio-E biological emergency mitigation tool are demonstrated. PMID:25419503

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

System on chip module configured for event-driven architecture

DOEpatents

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

2017-10-17

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

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

PubMed Central

2011-01-01

Background Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology. Result We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site. This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser. Conclusions Targeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in http://tools.proteomecenter.org/ATAQS/ATAQS.html PMID:21414234

[Relevance of big data for molecular diagnostics].

PubMed

Bonin-Andresen, M; Smiljanovic, B; Stuhlmüller, B; Sörensen, T; Grützkau, A; Häupl, T

2018-04-01

Big data analysis raises the expectation that computerized algorithms may extract new knowledge from otherwise unmanageable vast data sets. What are the algorithms behind the big data discussion? In principle, high throughput technologies in molecular research already introduced big data and the development and application of analysis tools into the field of rheumatology some 15 years ago. This includes especially omics technologies, such as genomics, transcriptomics and cytomics. Some basic methods of data analysis are provided along with the technology, however, functional analysis and interpretation requires adaptation of existing or development of new software tools. For these steps, structuring and evaluating according to the biological context is extremely important and not only a mathematical problem. This aspect has to be considered much more for molecular big data than for those analyzed in health economy or epidemiology. Molecular data are structured in a first order determined by the applied technology and present quantitative characteristics that follow the principles of their biological nature. These biological dependencies have to be integrated into software solutions, which may require networks of molecular big data of the same or even different technologies in order to achieve cross-technology confirmation. More and more extensive recording of molecular processes also in individual patients are generating personal big data and require new strategies for management in order to develop data-driven individualized interpretation concepts. With this perspective in mind, translation of information derived from molecular big data will also require new specifications for education and professional competence.

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

PubMed

Morgan, Matthew; Mates, Jonathan; Chang, Paul

2006-09-01

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

The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati

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

PubMed Central

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

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

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

PubMed

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

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

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

PubMed Central

2009-01-01

Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://genome.tugraz.at/iLAP/. Conclusion iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community. PMID:19941647

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

PubMed

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

2011-04-28

Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We demonstrate it's usefulness using the example of a signaling cascade leading to formation of a morphological gradient of Fus3 within the cytoplasm of the mating yeast cell Saccharomyces cerevisiae. STSE is an efficient and powerful novel platform, designed for computational handling and evaluation of microscopic images. It allows for an uninterrupted workflow including digitization, representation, analysis, and mathematical modeling. By providing the means to relate the simulation to the image data it allows for systematic, image driven model validation or rejection. STSE can be scripted and extended using the Python language. STSE should be considered rather as an API together with workflow guidelines and a collection of GUI tools than a stand alone application. The priority of the project is to provide an easy and intuitive way of extending and customizing software using the Python language.

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

NASA Technical Reports Server (NTRS)

King, Ellis; Hart, Jeremy; Odegard, Ryan

2010-01-01

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

Machine learning and data science in soft materials engineering

NASA Astrophysics Data System (ADS)

Ferguson, Andrew L.

2018-01-01

In many branches of materials science it is now routine to generate data sets of such large size and dimensionality that conventional methods of analysis fail. Paradigms and tools from data science and machine learning can provide scalable approaches to identify and extract trends and patterns within voluminous data sets, perform guided traversals of high-dimensional phase spaces, and furnish data-driven strategies for inverse materials design. This topical review provides an accessible introduction to machine learning tools in the context of soft and biological materials by ‘de-jargonizing’ data science terminology, presenting a taxonomy of machine learning techniques, and surveying the mathematical underpinnings and software implementations of popular tools, including principal component analysis, independent component analysis, diffusion maps, support vector machines, and relative entropy. We present illustrative examples of machine learning applications in soft matter, including inverse design of self-assembling materials, nonlinear learning of protein folding landscapes, high-throughput antimicrobial peptide design, and data-driven materials design engines. We close with an outlook on the challenges and opportunities for the field.

Machine learning and data science in soft materials engineering.

PubMed

Ferguson, Andrew L

2018-01-31

In many branches of materials science it is now routine to generate data sets of such large size and dimensionality that conventional methods of analysis fail. Paradigms and tools from data science and machine learning can provide scalable approaches to identify and extract trends and patterns within voluminous data sets, perform guided traversals of high-dimensional phase spaces, and furnish data-driven strategies for inverse materials design. This topical review provides an accessible introduction to machine learning tools in the context of soft and biological materials by 'de-jargonizing' data science terminology, presenting a taxonomy of machine learning techniques, and surveying the mathematical underpinnings and software implementations of popular tools, including principal component analysis, independent component analysis, diffusion maps, support vector machines, and relative entropy. We present illustrative examples of machine learning applications in soft matter, including inverse design of self-assembling materials, nonlinear learning of protein folding landscapes, high-throughput antimicrobial peptide design, and data-driven materials design engines. We close with an outlook on the challenges and opportunities for the field.

Test Driven Development of Scientific Models

NASA Technical Reports Server (NTRS)

Clune, Thomas L.

2012-01-01

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

Ten recommendations for software engineering in research.

PubMed

Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph

2014-01-01

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

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

ERIC Educational Resources Information Center

Buffardi, Kevin John

2014-01-01

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

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

NASA Tech Briefs, January 2004

NASA Technical Reports Server (NTRS)

2004-01-01

Topics covered include: Multisensor Instrument for Real-Time Biological Monitoring; Sensor for Monitoring Nanodevice-Fabrication Plasmas; Backed Bending Actuator; Compact Optoelectronic Compass; Micro Sun Sensor for Spacecraft; Passive IFF: Autonomous Nonintrusive Rapid Identification of Friendly Assets; Finned-Ladder Slow-Wave Circuit for a TWT; Directional Radio-Frequency Identification Tag Reader; Integrated Solar-Energy-Harvesting and -Storage Device; Event-Driven Random-Access-Windowing CCD Imaging System; Stroboscope Controller for Imaging Helicopter Rotors; Software for Checking State-charts; Program Predicts Broadband Noise from a Turbofan Engine; Protocol for a Delay-Tolerant Data-Communication Network; Software Implements a Space-Mission File-Transfer Protocol; Making Carbon-Nanotube Arrays Using Block Copolymers: Part 2; Modular Rake of Pitot Probes; Preloading To Accelerate Slow-Crack-Growth Testing; Miniature Blimps for Surveillance and Collection of Samples; Hybrid Automotive Engine Using Ethanol-Burning Miller Cycle; Fabricating Blazed Diffraction Gratings by X-Ray Lithography; Freeze-Tolerant Condensers; The StarLight Space Interferometer; Champagne Heat Pump; Controllable Sonar Lenses and Prisms Based on ERFs; Measuring Gravitation Using Polarization Spectroscopy; Serial-Turbo-Trellis-Coded Modulation with Rate-1 Inner Code; Enhanced Software for Scheduling Space-Shuttle Processing; Bayesian-Augmented Identification of Stars in a Narrow View; Spacecraft Orbits for Earth/Mars-Lander Radio Relay; and Self-Inflatable/Self-Rigidizable Reflectarray Antenna.

Behavior driven testing in ALMA telescope calibration software

NASA Astrophysics Data System (ADS)

Gil, Juan P.; Garces, Mario; Broguiere, Dominique; Shen, Tzu-Chiang

2016-07-01

ALMA software development cycle includes well defined testing stages that involves developers, testers and scientists. We adapted Behavior Driven Development (BDD) to testing activities applied to Telescope Calibration (TELCAL) software. BDD is an agile technique that encourages communication between roles by defining test cases using natural language to specify features and scenarios, what allows participants to share a common language and provides a high level set of automated tests. This work describes how we implemented and maintain BDD testing for TELCAL, the infrastructure needed to support it and proposals to expand this technique to other subsystems.

Simplified pulse reactor for real-time long-term in vitro testing of biological heart valves.

PubMed

Schleicher, Martina; Sammler, Günther; Schmauder, Michael; Fritze, Olaf; Huber, Agnes J; Schenke-Layland, Katja; Ditze, Günter; Stock, Ulrich A

2010-05-01

Long-term function of biological heart valve prostheses (BHV) is limited by structural deterioration leading to failure with associated arterial hypertension. The objective of this work was development of an easy to handle real-time pulse reactor for evaluation of biological and tissue engineered heart valves under different pressures and long-term conditions. The pulse reactor was made of medical grade materials for placement in a 37 degrees C incubator. Heart valves were mounted in a housing disc moving horizontally in culture medium within a cylindrical culture reservoir. The microprocessor-controlled system was driven by pressure resulting in a cardiac-like cycle enabling competent opening and closing of the leaflets with adjustable pulse rates and pressures between 0.25 to 2 Hz and up to 180/80 mmHg, respectively. A custom-made imaging system with an integrated high-speed camera and image processing software allow calculation of effective orifice areas during cardiac cycle. This simple pulse reactor design allows reproducible generation of patient-like pressure conditions and data collection during long-term experiments.

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

NASA Technical Reports Server (NTRS)

Evensen, Kenneth D.; Weiss, Kathryn Anne

2010-01-01

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

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.

Measuring the software process and product: Lessons learned in the SEL

NASA Technical Reports Server (NTRS)

Basili, V. R.

1985-01-01

The software development process and product can and should be measured. The software measurement process at the Software Engineering Laboratory (SEL) has taught a major lesson: develop a goal-driven paradigm (also characterized as a goal/question/metric paradigm) for data collection. Project analysis under this paradigm leads to a design for evaluating and improving the methodology of software development and maintenance.

Bar-Code System for a Microbiological Laboratory

NASA Technical Reports Server (NTRS)

Law, Jennifer; Kirschner, Larry

2007-01-01

A bar-code system has been assembled for a microbiological laboratory that must examine a large number of samples. The system includes a commercial bar-code reader, computer hardware and software components, plus custom-designed database software. The software generates a user-friendly, menu-driven interface.

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

ERIC Educational Resources Information Center

Brown, Mary Erin

2013-01-01

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

The State of the Human Proteome in 2013 as viewed through PeptideAtlas: Comparing the Kidney, Urine, and Plasma Proteomes for the Biology and Disease-driven Human Proteome Project

PubMed Central

Farrah, Terry; Deutsch, Eric W.; Omenn, Gilbert S.; Sun, Zhi; Watts, Julian D.; Yamamoto, Tadashi; Shteynberg, David; Harris, Micheleen M.; Moritz, Robert L.

2014-01-01

The kidney, urine, and plasma proteomes are intimately related: proteins and metabolic waste products are filtered from the plasma by the kidney and excreted via the urine, while kidney proteins may be secreted into the circulation or released into the urine. Shotgun proteomics datasets derived from human kidney, urine, and plasma samples were collated and processed using a uniform software pipeline, and relative protein abundances were estimated by spectral counting. The resulting PeptideAtlas builds yielded 4005, 2491, and 3553 nonredundant proteins at 1% FDR for the kidney, urine, and plasma proteomes, respectively—for kidney and plasma, the largest high-confidence protein sets to date. The same pipeline applied to all available human data yielded a 2013 Human PeptideAtlas build containing 12,644 nonredundant proteins and at least one peptide for each of ~14,000 Swiss-Prot entries, an increase over 2012 of ~7.5% of the predicted human proteome. We demonstrate that abundances are correlated between plasma and urine, examine the most abundant urine proteins not derived from either plasma or kidney, and consider the biomarker potential of proteins associated with renal decline. This analysis forms part of the Biology and Disease-driven Human Proteome Project (B/D-HPP) and a contribution to the Chromosome-centric Human Proteome Project (C-HPP) special issue. PMID:24261998

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

PubMed

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

2017-02-01

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

Clustering and Network Analysis of Reverse Phase Protein Array Data.

PubMed

Byron, Adam

2017-01-01

Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets. Here, two approaches for the computational analysis of RPPA data are detailed: the identification of similar patterns of protein expression by hierarchical cluster analysis and the modeling of protein interactions and signaling relationships by network analysis. The protocols use freely available, cross-platform software, are easy to implement, and do not require any programming expertise. Serving as data-driven starting points for further in-depth analysis, validation, and biological experimentation, these and related bioinformatic approaches can accelerate the functional interpretation of RPPA data.

Flight dynamics system software development environment (FDS/SDE) tutorial

NASA Technical Reports Server (NTRS)

Buell, John; Myers, Philip

1986-01-01

A sample development scenario using the Flight Dynamics System Software Development Environment (FDS/SDE) is presented. The SDE uses a menu-driven, fill-in-the-blanks format that provides online help at all steps, thus eliminating lengthy training and allowing immediate use of this new software development tool.

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

NASA Astrophysics Data System (ADS)

Buettner, Douglas John

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

Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.

PubMed

Eppig, Janan T; Smith, Cynthia L; Blake, Judith A; Ringwald, Martin; Kadin, James A; Richardson, Joel E; Bult, Carol J

2017-01-01

The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.

A Menu-Driven Interface to Unix-Based Resources

PubMed Central

Evans, Elizabeth A.

1989-01-01

Unix has often been overlooked in the past as a viable operating system for anyone other than computer scientists. Its terseness, non-mnemonic nature of the commands, and the lack of user-friendly software to run under it are but a few of the user-related reasons which have been cited. It is, nevertheless, the operating system of choice in many cases. This paper describes a menu-driven interface to Unix which provides user-friendlier access to the software resources available on the computers running under Unix.

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

NASA Astrophysics Data System (ADS)

Oliveira, Micael

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

Aspect-Oriented Model-Driven Software Product Line Engineering

NASA Astrophysics Data System (ADS)

Groher, Iris; Voelter, Markus

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

Thyroid Cancer and Tumor Collaborative Registry (TCCR).

PubMed

Shats, Oleg; Goldner, Whitney; Feng, Jianmin; Sherman, Alexander; Smith, Russell B; Sherman, Simon

2016-01-01

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC.

Towards Model-Driven End-User Development in CALL

ERIC Educational Resources Information Center

Farmer, Rod; Gruba, Paul

2006-01-01

The purpose of this article is to introduce end-user development (EUD) processes to the CALL software development community. EUD refers to the active participation of end-users, as non-professional developers, in the software development life cycle. Unlike formal software engineering approaches, the focus in EUD on means/ends development is…

Application Development Methodology Appropriateness: An Exploratory Case Study Bridging the Gap between Framework Characteristics and Selection

ERIC Educational Resources Information Center

Williams, Lawrence H., Jr.

2013-01-01

This qualitative study analyzed experiences of twenty software developers. The research showed that all software development methodologies are distinct from each other. While some, such as waterfall, focus on traditional, plan-driven approaches that allow software requirements and design to evolve; others facilitate ambiguity and uncertainty by…

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

NASA Astrophysics Data System (ADS)

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

2002-09-01

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

An Analysis of Category Management of Service Contracts

DTIC Science & Technology

2017-12-01

management teams a way to make informed , data-driven decisions. Data-driven decisions derived from clustering not only align with Category...savings. Furthermore, this methodology provides a data-driven visualization to inform sound business decisions on potential Category Management ...Category Management initiatives. The Maptitude software will allow future research to collect data and develop visualizations to inform Category

Data-driven traffic impact assessment tool for work zones.

DOT National Transportation Integrated Search

2017-03-01

Traditionally, traffic impacts of work zones have been assessed using planning software such as Quick Zone, custom spreadsheets, and others. These software programs generate delay, queuing, and other mobility measures but are difficult to validate du...

Test Driven Development of Scientific Models

NASA Technical Reports Server (NTRS)

Clune, Thomas L.

2014-01-01

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

Architecture for interoperable software in biology.

PubMed

Bare, James Christopher; Baliga, Nitin S

2014-07-01

Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. To this end, simple flexible strategies are needed for interconnecting heterogeneous software tools and enabling data exchange between them. Drawing on our own work and that of others, we present several strategies for interoperability and their consequences, in particular, a set of simple data structures--list, matrix, network, table and tuple--that have proven sufficient to achieve a high degree of interoperability. We provide a few guidelines for the development of future software that will function as part of an interoperable community of software tools for biological data analysis and visualization. © The Author 2012. Published by Oxford University Press.

Technology-driven dietary assessment: a software developer’s perspective

PubMed Central

Buday, Richard; Tapia, Ramsey; Maze, Gary R.

2015-01-01

Dietary researchers need new software to improve nutrition data collection and analysis, but creating information technology is difficult. Software development projects may be unsuccessful due to inadequate understanding of needs, management problems, technology barriers or legal hurdles. Cost overruns and schedule delays are common. Barriers facing scientific researchers developing software include workflow, cost, schedule, and team issues. Different methods of software development and the role that intellectual property rights play are discussed. A dietary researcher must carefully consider multiple issues to maximize the likelihood of success when creating new software. PMID:22591224

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

NASA Astrophysics Data System (ADS)

Kumlander, Deniss

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

Test Driven Development: Lessons from a Simple Scientific Model

NASA Astrophysics Data System (ADS)

Clune, T. L.; Kuo, K.

2010-12-01

In the commercial software industry, unit testing frameworks have emerged as a disruptive technology that has permanently altered the process by which software is developed. Unit testing frameworks significantly reduce traditional barriers, both practical and psychological, to creating and executing tests that verify software implementations. A new development paradigm, known as test driven development (TDD), has emerged from unit testing practices, in which low-level tests (i.e. unit tests) are created by developers prior to implementing new pieces of code. Although somewhat counter-intuitive, this approach actually improves developer productivity. In addition to reducing the average time for detecting software defects (bugs), the requirement to provide procedure interfaces that enable testing frequently leads to superior design decisions. Although TDD is widely accepted in many software domains, its applicability to scientific modeling still warrants reasonable skepticism. While the technique is clearly relevant for infrastructure layers of scientific models such as the Earth System Modeling Framework (ESMF), numerical and scientific components pose a number of challenges to TDD that are not often encountered in commercial software. Nonetheless, our experience leads us to believe that the technique has great potential not only for developer productivity, but also as a tool for understanding and documenting the basic scientific assumptions upon which our models are implemented. We will provide a brief introduction to test driven development and then discuss our experience in using TDD to implement a relatively simple numerical model that simulates the growth of snowflakes. Many of the lessons learned are directly applicable to larger scientific models.

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.

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

PubMed

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

2011-04-15

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

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

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

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

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

PubMed

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

2012-06-28

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

PomBase: a comprehensive online resource for fission yeast

PubMed Central

Wood, Valerie; Harris, Midori A.; McDowall, Mark D.; Rutherford, Kim; Vaughan, Brendan W.; Staines, Daniel M.; Aslett, Martin; Lock, Antonia; Bähler, Jürg; Kersey, Paul J.; Oliver, Stephen G.

2012-01-01

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance. PMID:22039153

Biology-driven library design for probe discovery.

PubMed

Inglese, James; Hasson, Samuel A

2011-10-28

Libraries of diverse small molecules are important to probe and drug discovery. The current trend toward building massive screening collections to support drug development, a special application of chemical biology, can limit their broader potential. Biology-driven construction methods (Wallace et al., 2011) are rapidly emerging to bring chemical libraries back on a viable path. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

ERIC Educational Resources Information Center

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

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Model driven development of clinical information sytems using openEHR.

PubMed

Atalag, Koray; Yang, Hong Yul; Tempero, Ewan; Warren, Jim

2011-01-01

openEHR and the recent international standard (ISO 13606) defined a model driven software development methodology for health information systems. However there is little evidence in the literature describing implementation; especially for desktop clinical applications. This paper presents an implementation pathway using .Net/C# technology for Microsoft Windows desktop platforms. An endoscopy reporting application driven by openEHR Archetypes and Templates has been developed. A set of novel GUI directives has been defined and presented which guides the automatic graphical user interface generator to render widgets properly. We also reveal the development steps and important design decisions; from modelling to the final software product. This might provide guidance for other developers and form evidence required for the adoption of these standards for vendors and national programs alike.

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

Computer-Based Semantic Network in Molecular Biology: A Demonstration.

ERIC Educational Resources Information Center

Callman, Joshua L.; And Others

This paper analyzes the hardware and software features that would be desirable in a computer-based semantic network system for representing biology knowledge. It then describes in detail a prototype network of molecular biology knowledge that has been developed using Filevision software and a Macintosh computer. The prototype contains about 100…

Computer Aided Teaching of Digital Signal Processing.

ERIC Educational Resources Information Center

Castro, Ian P.

1990-01-01

Describes a microcomputer-based software package developed at the University of Surrey for teaching digital signal processing to undergraduate science and engineering students. Menu-driven software capabilities are explained, including demonstration of qualitative concepts and experimentation with quantitative data, and examples are given of…

Software For Computing Reliability Of Other Software

NASA Technical Reports Server (NTRS)

Nikora, Allen; Antczak, Thomas M.; Lyu, Michael

1995-01-01

Computer Aided Software Reliability Estimation (CASRE) computer program developed for use in measuring reliability of other software. Easier for non-specialists in reliability to use than many other currently available programs developed for same purpose. CASRE incorporates mathematical modeling capabilities of public-domain Statistical Modeling and Estimation of Reliability Functions for Software (SMERFS) computer program and runs in Windows software environment. Provides menu-driven command interface; enabling and disabling of menu options guides user through (1) selection of set of failure data, (2) execution of mathematical model, and (3) analysis of results from model. Written in C language.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Efficient key pathway mining: combining networks and OMICS data.

PubMed

Alcaraz, Nicolas; Friedrich, Tobias; Kötzing, Timo; Krohmer, Anton; Müller, Joachim; Pauling, Josch; Baumbach, Jan

2012-07-01

Systems biology has emerged over the last decade. Driven by the advances in sophisticated measurement technology the research community generated huge molecular biology data sets. These comprise rather static data on the interplay of biological entities, for instance protein-protein interaction network data, as well as quite dynamic data collected for studying the behavior of individual cells or tissues in accordance with changing environmental conditions, such as DNA microarrays or RNA sequencing. Here we bring the two different data types together in order to gain higher level knowledge. We introduce a significantly improved version of the KeyPathwayMiner software framework. Given a biological network modelled as a graph and a set of expression studies, KeyPathwayMiner efficiently finds and visualizes connected sub-networks where most components are expressed in most cases. It finds all maximal connected sub-networks where all nodes but k exceptions are expressed in all experimental studies but at most l exceptions. We demonstrate the power of the new approach by comparing it to similar approaches with gene expression data previously used to study Huntington's disease. In addition, we demonstrate KeyPathwayMiner's flexibility and applicability to non-array data by analyzing genome-scale DNA methylation profiles from colorectal tumor cancer patients. KeyPathwayMiner release 2 is available as a Cytoscape plugin and online at http://keypathwayminer.mpi-inf.mpg.de.

Thyroid Cancer and Tumor Collaborative Registry (TCCR)

PubMed Central

Shats, Oleg; Goldner, Whitney; Feng, Jianmin; Sherman, Alexander; Smith, Russell B.; Sherman, Simon

2016-01-01

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC. PMID:27168721

FATSLiM: a fast and robust software to analyze MD simulations of membranes.

PubMed

Buchoux, Sébastien

2017-01-01

When studying biological membranes, Molecular Dynamics (MD) simulations reveal to be quite complementary to experimental techniques. Because the simulated systems keep increasing both in size and complexity, the analysis of MD trajectories need to be computationally efficient while being robust enough to perform analysis on membranes that may be curved or deformed due to their size and/or protein-lipid interactions. This work presents a new software named FATSLiM ('Fast Analysis Toolbox for Simulations of Lipid Membranes') that can extract physical properties from MD simulations of membranes (with or without interacting proteins). Because it relies on the calculation of local normals, FATSLiM does not depend of the bilayer morphology and thus can handle with the same accuracy vesicles for instance. Thanks to an efficiency-driven development, it is also fast and consumes a rather low amount of memory. FATSLiM (http://fatslim.github.io) is a stand-alone software written in Python. Source code is released under the GNU GPLv3 and is freely available at https://github.com/FATSLiM/fatslim A complete online documentation including instructions for platform-independent installation is available at http://pythonhosted.org/fatslim CONTACT: sebastien.buchoux@u-picardie.frSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Reviews: Software.

ERIC Educational Resources Information Center

Mackenzie, Norma N.; And Others

1988-01-01

Reviews four computer software packages including: "The Physical Science Series: Sound" which demonstrates making waves, speed of sound, doppler effect, and human hearing; "Andromeda" depicting celestial motions in any direction; "Biology Quiz: Humans" covering chemistry, cells, viruses, and human biology; and…

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

ERIC Educational Resources Information Center

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

2016-01-01

Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ~5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and…

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

PubMed

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

2012-06-01

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

Stellar Inertial Navigation Workstation

NASA Technical Reports Server (NTRS)

Johnson, W.; Johnson, B.; Swaminathan, N.

1989-01-01

Software and hardware assembled to support specific engineering activities. Stellar Inertial Navigation Workstation (SINW) is integrated computer workstation providing systems and engineering support functions for Space Shuttle guidance and navigation-system logistics, repair, and procurement activities. Consists of personal-computer hardware, packaged software, and custom software integrated together into user-friendly, menu-driven system. Designed to operate on IBM PC XT. Applied in business and industry to develop similar workstations.

The Need for Software Architecture Evaluation in the Acquisition of Software-Intensive Sysetms

DTIC Science & Technology

2014-01-01

Function and Performance Specification GIG Global Information Grid ISO International Standard Organisation MDA Model Driven Architecture...architecture and design, which is a key part of knowledge-based economy UNCLASSIFIED DSTO-TR-2936 UNCLASSIFIED 24  Allow Australian SMEs to

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

PubMed

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

2004-06-01

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

Toward an integrated software platform for systems pharmacology

PubMed Central

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

2013-01-01

Understanding complex biological systems requires the extensive support of computational tools. This is particularly true for systems pharmacology, which aims to understand the action of drugs and their interactions in a systems context. Computational models play an important role as they can be viewed as an explicit representation of biological hypotheses to be tested. A series of software and data resources are used for model development, verification and exploration of the possible behaviors of biological systems using the model that may not be possible or not cost effective by experiments. Software platforms play a dominant role in creativity and productivity support and have transformed many industries, techniques that can be applied to biology as well. Establishing an integrated software platform will be the next important step in the field. © 2013 The Authors. Biopharmaceutics & Drug Disposition published by John Wiley & Sons, Ltd. PMID:24150748

GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes

PubMed Central

Altermann, Eric; Lu, Jingli; McCulloch, Alan

2017-01-01

Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use. PMID:28386247

GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes.

PubMed

Altermann, Eric; Lu, Jingli; McCulloch, Alan

2017-01-01

Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.

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

PubMed

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

2013-04-22

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

Variability in physical and biological exchange among coastal wetlands and their adjacent Great Lakes

EPA Science Inventory

Hydrology is a major governor of physically-driven exchange among coastal wetlands and the adjacent Great Lake, whereas fish movement is a major governor of biologically-driven exchange. We use data describing coastal wetland morphology, hydrology, water quality, and fish tissue...

Synthetic Peptide Arrays for Pathway-Level Protein Monitoring by Liquid Chromatography-Tandem Mass Spectrometry*

PubMed Central

Hewel, Johannes A.; Liu, Jian; Onishi, Kento; Fong, Vincent; Chandran, Shamanta; Olsen, Jonathan B.; Pogoutse, Oxana; Schutkowski, Mike; Wenschuh, Holger; Winkler, Dirk F. H.; Eckler, Larry; Zandstra, Peter W.; Emili, Andrew

2010-01-01

Effective methods to detect and quantify functionally linked regulatory proteins in complex biological samples are essential for investigating mammalian signaling pathways. Traditional immunoassays depend on proprietary reagents that are difficult to generate and multiplex, whereas global proteomic profiling can be tedious and can miss low abundance proteins. Here, we report a target-driven liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategy for selectively examining the levels of multiple low abundance components of signaling pathways which are refractory to standard shotgun screening procedures and hence appear limited in current MS/MS repositories. Our stepwise approach consists of: (i) synthesizing microscale peptide arrays, including heavy isotope-labeled internal standards, for use as high quality references to (ii) build empirically validated high density LC-MS/MS detection assays with a retention time scheduling system that can be used to (iii) identify and quantify endogenous low abundance protein targets in complex biological mixtures with high accuracy by correlation to a spectral database using new software tools. The method offers a flexible, rapid, and cost-effective means for routine proteomic exploration of biological systems including “label-free” quantification, while minimizing spurious interferences. As proof-of-concept, we have examined the abundance of transcription factors and protein kinases mediating pluripotency and self-renewal in embryonic stem cell populations. PMID:20467045

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

DTIC Science & Technology

2004-06-01

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

Improving Reuse in Software Development for the Life Sciences

ERIC Educational Resources Information Center

Iannotti, Nicholas V.

2013-01-01

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

Implementation of a deidentified federated data network for population-based cohort discovery

PubMed Central

Abend, Aaron; Mandel, Aaron; Geraghty, Estella; Gabriel, Davera; Wynden, Rob; Kamerick, Michael; Anderson, Kent; Rainwater, Julie; Tarczy-Hornoch, Peter

2011-01-01

Objective The Cross-Institutional Clinical Translational Research project explored a federated query tool and looked at how this tool can facilitate clinical trial cohort discovery by managing access to aggregate patient data located within unaffiliated academic medical centers. Methods The project adapted software from the Informatics for Integrating Biology and the Bedside (i2b2) program to connect three Clinical Translational Research Award sites: University of Washington, Seattle, University of California, Davis, and University of California, San Francisco. The project developed an iterative spiral software development model to support the implementation and coordination of this multisite data resource. Results By standardizing technical infrastructures, policies, and semantics, the project enabled federated querying of deidentified clinical datasets stored in separate institutional environments and identified barriers to engaging users for measuring utility. Discussion The authors discuss the iterative development and evaluation phases of the project and highlight the challenges identified and the lessons learned. Conclusion The common system architecture and translational processes provide high-level (aggregate) deidentified access to a large patient population (>5 million patients), and represent a novel and extensible resource. Enhancing the network for more focused disease areas will require research-driven partnerships represented across all partner sites. PMID:21873473

Implementation of a deidentified federated data network for population-based cohort discovery.

PubMed

Anderson, Nicholas; Abend, Aaron; Mandel, Aaron; Geraghty, Estella; Gabriel, Davera; Wynden, Rob; Kamerick, Michael; Anderson, Kent; Rainwater, Julie; Tarczy-Hornoch, Peter

2012-06-01

The Cross-Institutional Clinical Translational Research project explored a federated query tool and looked at how this tool can facilitate clinical trial cohort discovery by managing access to aggregate patient data located within unaffiliated academic medical centers. The project adapted software from the Informatics for Integrating Biology and the Bedside (i2b2) program to connect three Clinical Translational Research Award sites: University of Washington, Seattle, University of California, Davis, and University of California, San Francisco. The project developed an iterative spiral software development model to support the implementation and coordination of this multisite data resource. By standardizing technical infrastructures, policies, and semantics, the project enabled federated querying of deidentified clinical datasets stored in separate institutional environments and identified barriers to engaging users for measuring utility. The authors discuss the iterative development and evaluation phases of the project and highlight the challenges identified and the lessons learned. The common system architecture and translational processes provide high-level (aggregate) deidentified access to a large patient population (>5 million patients), and represent a novel and extensible resource. Enhancing the network for more focused disease areas will require research-driven partnerships represented across all partner sites.

Reuse-Driven Software Processes Guidebook. Version 02.00.03

DTIC Science & Technology

1993-11-01

a required sys - tem without unduly constraining the details of the solution. The Naval Research Laboratory Software Cost Reduction project developed...conventional manner. The emphasis is still on the development of "one-of-a-kind" sys - tems and the phased completion and review of corresponding...Application Engineering to improve the life-cycle productivity of Sy - 21 OVM ftrdauntals of Syatbes the total software development enterprise. The

Astronomy Software

NASA Technical Reports Server (NTRS)

1995-01-01

Software Bisque's TheSky, SkyPro and Remote Astronomy Software incorporate technology developed for the Hubble Space Telescope. TheSky and SkyPro work together to orchestrate locating, identifying and acquiring images of deep sky objects. With all three systems, the user can directly control computer-driven telescopes and charge coupled device (CCD) cameras through serial ports. Through the systems, astronomers and students can remotely operate a telescope at the Mount Wilson Observatory Institute.

Metadata-driven Delphi rating on the Internet.

PubMed

Deshpande, Aniruddha M; Shiffman, Richard N; Nadkarni, Prakash M

2005-01-01

Paper-based data collection and analysis for consensus development is inefficient and error-prone. Computerized techniques that could improve efficiency, however, have been criticized as costly, inconvenient and difficult to use. We designed and implemented a metadata-driven Web-based Delphi rating and analysis tool, employing the flexible entity-attribute-value schema to create generic, reusable software. The software can be applied to various domains by altering the metadata; the programming code remains intact. This approach greatly reduces the marginal cost of re-using the software. We implemented our software to prepare for the Conference on Guidelines Standardization. Twenty-three invited experts completed the first round of the Delphi rating on the Web. For each participant, the software generated individualized reports that described the median rating and the disagreement index (calculated from the Interpercentile Range Adjusted for Symmetry) as defined by the RAND/UCLA Appropriateness Method. We evaluated the software with a satisfaction survey using a five-level Likert scale. The panelists felt that Web data entry was convenient (median 4, interquartile range [IQR] 4.0-5.0), acceptable (median 4.5, IQR 4.0-5.0) and easily accessible (median 5, IQR 4.0-5.0). We conclude that Web-based Delphi rating for consensus development is a convenient and acceptable alternative to the traditional paper-based method.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs.

PubMed

Dayringer, H E; Sammons, S A

1991-04-01

Computer support for research in biotechnology has developed rapidly and has provided several tools to aid the researcher. This report describes the capabilities of new computer software developed in this laboratory to aid in the documentation and planning of experiments in molecular biology. The program, POLLUX, provides a graphical medium for the entry, edit and manipulation of DNA constructs and a textual format for display and edit of construct descriptive data. Program operation and procedures are designed to mimic the actual laboratory experiments with respect to capability and the order in which they are performed. Flexible control over the content of the computer-generated displays and program facilities is provided by a mouse-driven menu interface. Programmed facilities for mutagenesis, simulated cloning and searching of the database from networked workstations are described.

Model-Driven Development for PDS4 Software and Services

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Governing Software: Networks, Databases and Algorithmic Power in the Digital Governance of Public Education

ERIC Educational Resources Information Center

Williamson, Ben

2015-01-01

This article examines the emergence of "digital governance" in public education in England. Drawing on and combining concepts from software studies, policy and political studies, it identifies some specific approaches to digital governance facilitated by network-based communications and database-driven information processing software…

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

PubMed

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

2007-10-01

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

BRIDG: a domain information model for translational and clinical protocol-driven research.

PubMed

Becnel, Lauren B; Hastak, Smita; Ver Hoef, Wendy; Milius, Robert P; Slack, MaryAnn; Wold, Diane; Glickman, Michael L; Brodsky, Boris; Jaffe, Charles; Kush, Rebecca; Helton, Edward

2017-09-01

It is critical to integrate and analyze data from biological, translational, and clinical studies with data from health systems; however, electronic artifacts are stored in thousands of disparate systems that are often unable to readily exchange data. To facilitate meaningful data exchange, a model that presents a common understanding of biomedical research concepts and their relationships with health care semantics is required. The Biomedical Research Integrated Domain Group (BRIDG) domain information model fulfills this need. Software systems created from BRIDG have shared meaning "baked in," enabling interoperability among disparate systems. For nearly 10 years, the Clinical Data Standards Interchange Consortium, the National Cancer Institute, the US Food and Drug Administration, and Health Level 7 International have been key stakeholders in developing BRIDG. BRIDG is an open-source Unified Modeling Language-class model developed through use cases and harmonization with other models. With its 4+ releases, BRIDG includes clinical and now translational research concepts in its Common, Protocol Representation, Study Conduct, Adverse Events, Regulatory, Statistical Analysis, Experiment, Biospecimen, and Molecular Biology subdomains. The model is a Clinical Data Standards Interchange Consortium, Health Level 7 International, and International Standards Organization standard that has been utilized in national and international standards-based software development projects. It will continue to mature and evolve in the areas of clinical imaging, pathology, ontology, and vocabulary support. BRIDG 4.1.1 and prior releases are freely available at https://bridgmodel.nci.nih.gov . © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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.

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

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

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

Computer Center. Interactive Biology with Videodisc.

ERIC Educational Resources Information Center

Kramer, David W.

1991-01-01

Ways in which students are allowed to choose, based on their curiosity at the moment, which way they will move through a lesson are described. Available software for interactive biology programs and available authoring software for developing interactive programs by teachers and students are listed. (KR)

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.

Information Technology in University-Level Mathematics Teaching and Learning: A Mathematician's Point of View

ERIC Educational Resources Information Center

Borovik, Alexandre

2011-01-01

Although mathematicians frequently use specialist software in direct teaching of mathematics, as a means of delivery e-learning technologies have so far been less widely used. We (mathematicians) insist that teaching methods should be subject-specific and content-driven, not delivery-driven. We oppose generic approaches to teaching, including…

Model Driven Engineering with Ontology Technologies

NASA Astrophysics Data System (ADS)

Staab, Steffen; Walter, Tobias; Gröner, Gerd; Parreiras, Fernando Silva

Ontologies constitute formal models of some aspect of the world that may be used for drawing interesting logical conclusions even for large models. Software models capture relevant characteristics of a software artifact to be developed, yet, most often these software models have limited formal semantics, or the underlying (often graphical) software language varies from case to case in a way that makes it hard if not impossible to fix its semantics. In this contribution, we survey the use of ontology technologies for software modeling in order to carry over advantages from ontology technologies to the software modeling domain. It will turn out that ontology-based metamodels constitute a core means for exploiting expressive ontology reasoning in the software modeling domain while remaining flexible enough to accommodate varying needs of software modelers.

The Effects of Beacons, Comments, and Tasks on Program Comprehension Process in Software Maintenance

ERIC Educational Resources Information Center

Fan, Quyin

2010-01-01

Program comprehension is the most important and frequent process in software maintenance. Extensive research has found that individual characteristics of programmers, differences of computer programs, and differences of task-driven motivations are the major factors that affect the program comprehension results. There is no study specifically…

A new software-based architecture for quantum computer

NASA Astrophysics Data System (ADS)

Wu, Nan; Song, FangMin; Li, Xiangdong

2010-04-01

In this paper, we study a reliable architecture of a quantum computer and a new instruction set and machine language for the architecture, which can improve the performance and reduce the cost of the quantum computing. We also try to address some key issues in detail in the software-driven universal quantum computers.

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

PubMed

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

2015-08-21

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

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

PubMed

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

2017-11-14

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

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits.

PubMed

Fang, Hai; Knezevic, Bogdan; Burnham, Katie L; Knight, Julian C

2016-12-13

Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in medical genomics research, calling for efficient and integrative tools to resolve this problem. We introduce eXploring Genomic Relations (XGR), an open source tool designed for enhanced interpretation of genomic summary data enabling downstream knowledge discovery. Targeting users of varying computational skills, XGR utilises prior biological knowledge and relationships in a highly integrated but easily accessible way to make user-input genomic summary datasets more interpretable. We show how by incorporating ontology, annotation, and systems biology network-driven approaches, XGR generates more informative results than conventional analyses. We apply XGR to GWAS and eQTL summary data to explore the genomic landscape of the activated innate immune response and common immunological diseases. We provide genomic evidence for a disease taxonomy supporting the concept of a disease spectrum from autoimmune to autoinflammatory disorders. We also show how XGR can define SNP-modulated gene networks and pathways that are shared and distinct between diseases, how it achieves functional, phenotypic and epigenomic annotations of genes and variants, and how it enables exploring annotation-based relationships between genetic variants. XGR provides a single integrated solution to enhance interpretation of genomic summary data for downstream biological discovery. XGR is released as both an R package and a web-app, freely available at http://galahad.well.ox.ac.uk/XGR .

Integrative Systems Biology for Data Driven Knowledge Discovery

PubMed Central

Greene, Casey S.; Troyanskaya, Olga G.

2015-01-01

Integrative systems biology is an approach that brings together diverse high throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost effective manner. Using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of yet unknown components of a system of interest and how its malfunction leads to disease. PMID:21044756

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

PubMed Central

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

2009-01-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/. PMID:17707944

Software process improvement in the NASA software engineering laboratory

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

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

PubMed

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

2010-11-01

Both spatial and biological information are necessary in order to perform true optimization of a treatment plan and for predicting clinical outcome. The goal of this work is to develop an enhanced treatment plan evaluation tool which incorporates biological parameters and retains spatial dose information. A software system is developed which provides biological plan evaluation with a novel combination of features. It incorporates hyper-radiosensitivity using the induced-repair model and applies the new concept of dose convolution filter (DCF) to simulate dose wash-out effects due to cell migration, bystander effect, and/or tissue motion during treatment. Further, the concept of spatial DVH (sDVH) is introduced to evaluate and potentially optimize the spatial dose distribution in the target volume. Finally, generalized equivalent uniform dose is derived from both the physical dose distribution (gEUD) and the distribution of equivalent dose in 2 Gy fractions (gEUD2) and the software provides three separate models for calculation of tumor control probability (TCP), normal tissue complication probability (NTCP), and probability of uncomplicated tumor control (P+). TCP, NTCP, and P+ are provided as a function of prescribed dose and multivariable TCP, NTCP, and P+ plots are provided to illustrate the dependence on individual parameters used to calculate these quantities. Ten plans from two clinical treatment sites are selected to test the three calculation models provided by this software. By retaining both spatial and biological information about the dose distribution, the software is able to distinguish features of radiotherapy treatment plans not discernible using commercial systems. Plans that have similar DVHs may have different spatial and biological characteristics and the application of novel tools such as sDVH and DCF within the software may substantially change the apparent plan quality or predicted plan metrics such as TCP and NTCP. For the cases examined, both the calculation method and the application of DCF can change the ranking order of competing plans. The voxel-by-voxel TCP model makes it feasible to incorporate spatial variations of clonogen densities (n), radiosensitivities (SF2), and fractionation sensitivities (alpha/beta) as those data become available. The new software incorporates both spatial and biological information into the treatment planning process. The application of multiple methods for the incorporation of biological and spatial information has demonstrated that the order of application of biological models can change the order of plan ranking. Thus, the results of plan evaluation and optimization are dependent not only on the models used but also on the order in which they are applied. This software can help the planner choose more biologically optimal treatment plans and potentially predict treatment outcome more accurately.

Bioconductor: open software development for computational biology and bioinformatics

PubMed Central

Gentleman, Robert C; Carey, Vincent J; Bates, Douglas M; Bolstad, Ben; Dettling, Marcel; Dudoit, Sandrine; Ellis, Byron; Gautier, Laurent; Ge, Yongchao; Gentry, Jeff; Hornik, Kurt; Hothorn, Torsten; Huber, Wolfgang; Iacus, Stefano; Irizarry, Rafael; Leisch, Friedrich; Li, Cheng; Maechler, Martin; Rossini, Anthony J; Sawitzki, Gunther; Smith, Colin; Smyth, Gordon; Tierney, Luke; Yang, Jean YH; Zhang, Jianhua

2004-01-01

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples. PMID:15461798

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

PubMed

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

2018-02-20

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

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

PubMed Central

Navet, Nicolas; Havet, Lionel

2018-01-01

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

Changes in ocean circulation and carbon storage are decoupled from air-sea CO2 fluxes

NASA Astrophysics Data System (ADS)

Marinov, I.; Gnanadesikan, A.

2011-02-01

The spatial distribution of the air-sea flux of carbon dioxide is a poor indicator of the underlying ocean circulation and of ocean carbon storage. The weak dependence on circulation arises because mixing-driven changes in solubility-driven and biologically-driven air-sea fluxes largely cancel out. This cancellation occurs because mixing driven increases in the poleward residual mean circulation result in more transport of both remineralized nutrients and heat from low to high latitudes. By contrast, increasing vertical mixing decreases the storage associated with both the biological and solubility pumps, as it decreases remineralized carbon storage in the deep ocean and warms the ocean as a whole.

Changes in ocean circulation and carbon storage are decoupled from air-sea CO2 fluxes

NASA Astrophysics Data System (ADS)

Marinov, I.; Gnanadesikan, A.

2010-11-01

The spatial distribution of the air-sea flux of carbon dioxide is a poor indicator of the underlying ocean circulation and of ocean carbon storage. The weak dependence on circulation arises because mixing-driven changes in solubility-driven and biologically-driven air-sea fluxes largely cancel out. This cancellation occurs because mixing driven increases in the poleward residual mean circulation results in more transport of both remineralized nutrients and heat from low to high latitudes. By contrast, increasing vertical mixing decreases the storage associated with both the biological and solubility pumps, as it decreases remineralized carbon storage in the deep ocean and warms the ocean as a whole.

The State of Software for Evolutionary Biology

PubMed Central

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-01-01

Abstract 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. PMID:29385525

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

NASA Astrophysics Data System (ADS)

Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S. Jon; Garny, Alan; van Leeuwen, Ingeborg M. M.; Maini, Philip K.; Rodríguez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.

2009-12-01

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

Water Network Tool for Resilience v. 1.0

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

2015-12-09

WNTR is a python package designed to simulate and analyze resilience of water distribution networks. The software includes: - Pressure driven and demand driven hydraulic simulation - Water quality simulation to track concentration, trace, and water age - Conditional controls to simulate power outages - Models to simulate pipe breaks - A wide range of resilience metrics - Analysis and visualization tools

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

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

PubMed

Kibinge, Nelson; Ono, Naoaki; Horie, Masafumi; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Saito, Akira; Kanaya, Shigehiko

2016-06-01

Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation. The pipeline implements pathway-based modularization of expression profiles into functional units to improve biological interpretation. The integrated workflow was implemented as a web application software (TransReguloNet) with functions that enable pathway visualization and comparison of transcription factor activity between sample conditions defined in the experimental design. The pipeline merges differential expression, network construction, pathway-based abstraction, clustering and visualization. The framework was applied in analysis of actual expression datasets related to lung, breast and prostrate cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

PubMed Central

2011-01-01

Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified. Conclusions TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes. PMID:21333005

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-01-01

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

Architecture-led Requirements and Safety Analysis of an Aircraft Survivability Situational Awareness System

DTIC Science & Technology

2015-05-01

quality attributes. Prioritization of the utility tree leafs driven by mission goals help the user ensure that critical requirements are well-specified...Methods: State of the Art and Future Directions”, ACM Computing Surveys. 1996. 10 Laitenberger, Oliver , “A Survey of Software Inspection Technologies, Handbook on Software Engineering and Knowledge Engineering”. 2002.

Integrating Software-Architecture-Centric Methods into the Rational Unified Process

DTIC Science & Technology

2004-07-01

Architecture Design ...................................................................................... 19...QAW in a life- cycle context. One issue that needs to be addressed is how scenarios produced in a QAW can be used by a software architecture design method...implementation testing. 18 CMU/SEI-2004-TR-011 CMU/SEI-2004-TR-011 19 4 Architecture Design The Attribute-Driven Design (ADD) method

Toward Computational Cumulative Biology by Combining Models of Biological Datasets

PubMed Central

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

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database. PMID:25427176

Toward computational cumulative biology by combining models of biological datasets.

PubMed

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

2014-01-01

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

Comparing the Impacts of Tutorial and Edutainment Software Programs on Students' Achievements, Misconceptions, and Attitudes towards Biology

NASA Astrophysics Data System (ADS)

Kara, Yılmaz; Yeşilyurt, Selami

2008-02-01

The purpose of this study was to investigate the effects of tutorial and edutainment design of instructional software programs related to the "cell division" topic on student achievements, misconceptions and attitudes. An experimental research design including the cell division achievement test (CAT), the cell division concept test (CCT) and biology attitude scale (BAS) was applied at the beginning and at the end of the research. After the treatment, general achievement in CAT increased in favor of experimental groups. Instructional software programs also had the positive effect to the awareness of students' understandings to the general functions of mitosis and meiosis. However, the current study revealed that there were still some misconceptions in the experimental groups even after the treatment. It was also noticed that only using edutainment software program significantly changed students' attitudes towards biology.

Concept Map Value Propagation for Tactical Intelligence

DTIC Science & Technology

2007-06-01

meaningful diagrams: KMap, SmartDraw , MindGenius, and so on. However, CmapTools is the package we are using for this project. The software , produced by the...Cmap, driven by expected variability in the value of a datum and cost to get a new value. We use the CmapTools software developed with DoD support at... software developed with DoD support at the Institute of Human and Machine Cognition as a structural basis for creating and assessing tactical Cmaps. The

Cyber security best practices for the nuclear industry

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

Badr, I.

2012-07-01

When deploying software based systems, such as, digital instrumentation and controls for the nuclear industry, it is vital to include cyber security assessment as part of architecture and development process. When integrating and delivering software-intensive systems for the nuclear industry, engineering teams should make use of a secure, requirements driven, software development life cycle, ensuring security compliance and optimum return on investment. Reliability protections, data loss prevention, and privacy enforcement provide a strong case for installing strict cyber security policies. (authors)

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

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

Analyzing huge pathology images with open source software.

PubMed

Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

2013-06-06

Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272.

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272 PMID:23829479

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.

PubMed

Schmidt, Ellen M; Zhang, Ji; Zhou, Wei; Chen, Jin; Mohlke, Karen L; Chen, Y Eugene; Willer, Cristen J

2015-08-15

The majority of variation identified by genome wide association studies falls in non-coding genomic regions and is hypothesized to impact regulatory elements that modulate gene expression. Here we present a statistically rigorous software tool GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) for evaluating enrichment of any set of genetic variants with any set of regulatory features. Using variants from five phenotypes, we describe a data-driven approach to determine the tissue and cell types most relevant to a trait of interest and to identify the subset of regulatory features likely impacted by these variants. Last, we experimentally evaluate six predicted functional variants at six lipid-associated loci and demonstrate significant evidence for allele-specific impact on expression levels. GREGOR systematically evaluates enrichment of genetic variation with the vast collection of regulatory data available to explore novel biological mechanisms of disease and guide us toward the functional variant at trait-associated loci. GREGOR, including source code, documentation, examples, and executables, is available at http://genome.sph.umich.edu/wiki/GREGOR. cristen@umich.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Chaste: An Open Source C++ Library for Computational Physiology and Biology

PubMed Central

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

2013-01-01

Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials. PMID:23516352

Top 10 metrics for life science software good practices.

PubMed

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

2016-01-01

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

Top 10 metrics for life science software good practices

PubMed Central

2016-01-01

Metrics for assessing adoption of good development practices are a useful way to ensure that software is sustainable, reusable and functional. Sustainability means that the software used today will be available - and continue to be improved and supported - in the future. We report here an initial set of metrics that measure good practices in software development. This initiative differs from previously developed efforts in being a community-driven grassroots approach where experts from different organisations propose good software practices that have reasonable potential to be adopted by the communities they represent. We not only focus our efforts on understanding and prioritising good practices, we assess their feasibility for implementation and publish them here. PMID:27635232

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.

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

PubMed Central

Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

2011-01-01

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

Applying Computerized-Scoring Models of Written Biological Explanations across Courses and Colleges: Prospects and Limitations

PubMed Central

Ha, Minsu; Nehm, Ross H.; Urban-Lurain, Mark; Merrill, John E.

2011-01-01

Our study explored the prospects and limitations of using machine-learning software to score introductory biology students’ written explanations of evolutionary change. We investigated three research questions: 1) Do scoring models built using student responses at one university function effectively at another university? 2) How many human-scored student responses are needed to build scoring models suitable for cross-institutional application? 3) What factors limit computer-scoring efficacy, and how can these factors be mitigated? To answer these questions, two biology experts scored a corpus of 2556 short-answer explanations (from biology majors and nonmajors) at two universities for the presence or absence of five key concepts of evolution. Human- and computer-generated scores were compared using kappa agreement statistics. We found that machine-learning software was capable in most cases of accurately evaluating the degree of scientific sophistication in undergraduate majors’ and nonmajors’ written explanations of evolutionary change. In cases in which the software did not perform at the benchmark of “near-perfect” agreement (kappa > 0.80), we located the causes of poor performance and identified a series of strategies for their mitigation. Machine-learning software holds promise as an assessment tool for use in undergraduate biology education, but like most assessment tools, it is also characterized by limitations. PMID:22135372

Applying computerized-scoring models of written biological explanations across courses and colleges: prospects and limitations.

PubMed

Ha, Minsu; Nehm, Ross H; Urban-Lurain, Mark; Merrill, John E

2011-01-01

Our study explored the prospects and limitations of using machine-learning software to score introductory biology students' written explanations of evolutionary change. We investigated three research questions: 1) Do scoring models built using student responses at one university function effectively at another university? 2) How many human-scored student responses are needed to build scoring models suitable for cross-institutional application? 3) What factors limit computer-scoring efficacy, and how can these factors be mitigated? To answer these questions, two biology experts scored a corpus of 2556 short-answer explanations (from biology majors and nonmajors) at two universities for the presence or absence of five key concepts of evolution. Human- and computer-generated scores were compared using kappa agreement statistics. We found that machine-learning software was capable in most cases of accurately evaluating the degree of scientific sophistication in undergraduate majors' and nonmajors' written explanations of evolutionary change. In cases in which the software did not perform at the benchmark of "near-perfect" agreement (kappa > 0.80), we located the causes of poor performance and identified a series of strategies for their mitigation. Machine-learning software holds promise as an assessment tool for use in undergraduate biology education, but like most assessment tools, it is also characterized by limitations.

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

PubMed

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

2014-08-01

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

An exchange format for use-cases of hospital information systems.

PubMed

Masuda, G; Sakamoto, N; Sakai, R; Yamamoto, R

2001-01-01

Object-oriented software development is a powerful methodology for development of large hospital information systems. We think use-case driven approach is particularly useful for the development. In the use-cases driven approach, use-cases are documented at the first stage in the software development process and they are used through the whole steps in a variety of ways. Therefore, it is important to exchange and share the use-cases and make effective use of them through the overall lifecycle of a development process. In this paper, we propose a method of sharing and exchanging use-case models between applications, developers, and projects. We design an XML based exchange format for use-cases. We then discuss an application of the exchange format to support several software development activities. We preliminarily implemented a support system for object-oriented analysis based on the exchange format. The result shows that using the structural and semantic information in the exchange format enables the support system to assist the object-oriented analysis successfully.

A high-speed, large-capacity, 'jukebox' optical disk system

NASA Technical Reports Server (NTRS)

Ammon, G. J.; Calabria, J. A.; Thomas, D. T.

1985-01-01

Two optical disk 'jukebox' mass storage systems which provide access to any data in a store of 10 to the 13th bits (1250G bytes) within six seconds have been developed. The optical disk jukebox system is divided into two units, including a hardware/software controller and a disk drive. The controller provides flexibility and adaptability, through a ROM-based microcode-driven data processor and a ROM-based software-driven control processor. The cartridge storage module contains 125 optical disks housed in protective cartridges. Attention is given to a conceptual view of the disk drive unit, the NASA optical disk system, the NASA database management system configuration, the NASA optical disk system interface, and an open systems interconnect reference model.

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

PubMed

Clark, Kathleen

2011-07-01

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

Can a biologist fix a smartphone?-Just hack it!

PubMed

Kamoun, Sophien

2017-05-08

Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encoded in the genome sequence) and hardware (organism), genome editors can operate as software engineers to hack biological systems without any particularly deep understanding of the complexity of the systems.

Assessing the Effects of Tutorial and Edutainment Software Programs on Students' Achievements, Misconceptions and Attitudes towards Biology

ERIC Educational Resources Information Center

Kara, Yilmaz; Yesilyurt, Selami

2007-01-01

The purpose of this study was to investigate the effects of tutorial and edutainment software programs related to "genetic concepts" topic on student achievements, misconceptions and attitudes. An experimental research design including the genetic concepts achievement test (GAT), the genetic concept test (GCT) and biology attitude scale…

Biased and unbiased strategies to identify biologically active small molecules.

PubMed

Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

2014-08-15

Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. Copyright © 2014. Published by Elsevier Ltd.

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

NASA Astrophysics Data System (ADS)

Jones, Craig H.

2002-12-01

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

Building an Ontology-driven Database for Clinical Immune Research

PubMed Central

Ma, Jingming

2006-01-01

The clinical researches of immune response usually generate a huge amount of biomedical testing data over a certain period of time. The user-friendly data management systems based on the relational database will help immunologists/clinicians to fully manage the data. On the other hand, the same biological assays such as ELISPOT and flow cytometric assays are involved in immunological experiments no matter of different study purposes. The reuse of biological knowledge is one of driving forces behind this ontology-driven data management. Therefore, an ontology-driven database will help to handle different clinical immune researches and help immunologists/clinicians easily understand the immunological data from each other. We will discuss some outlines for building an ontology-driven data management for clinical immune researches (ODMim). PMID:17238637

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.

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

PubMed

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

2015-06-16

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

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eisenreich, Wolfgang; Dandekar, Thomas

2013-07-09

The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.

Federated ontology-based queries over cancer data

PubMed Central

2012-01-01

Background Personalised medicine provides patients with treatments that are specific to their genetic profiles. It requires efficient data sharing of disparate data types across a variety of scientific disciplines, such as molecular biology, pathology, radiology and clinical practice. Personalised medicine aims to offer the safest and most effective therapeutic strategy based on the gene variations of each subject. In particular, this is valid in oncology, where knowledge about genetic mutations has already led to new therapies. Current molecular biology techniques (microarrays, proteomics, epigenetic technology and improved DNA sequencing technology) enable better characterisation of cancer tumours. The vast amounts of data, however, coupled with the use of different terms - or semantic heterogeneity - in each discipline makes the retrieval and integration of information difficult. Results Existing software infrastructures for data-sharing in the cancer domain, such as caGrid, support access to distributed information. caGrid follows a service-oriented model-driven architecture. Each data source in caGrid is associated with metadata at increasing levels of abstraction, including syntactic, structural, reference and domain metadata. The domain metadata consists of ontology-based annotations associated with the structural information of each data source. However, caGrid's current querying functionality is given at the structural metadata level, without capitalising on the ontology-based annotations. This paper presents the design of and theoretical foundations for distributed ontology-based queries over cancer research data. Concept-based queries are reformulated to the target query language, where join conditions between multiple data sources are found by exploiting the semantic annotations. The system has been implemented, as a proof of concept, over the caGrid infrastructure. The approach is applicable to other model-driven architectures. A graphical user interface has been developed, supporting ontology-based queries over caGrid data sources. An extensive evaluation of the query reformulation technique is included. Conclusions To support personalised medicine in oncology, it is crucial to retrieve and integrate molecular, pathology, radiology and clinical data in an efficient manner. The semantic heterogeneity of the data makes this a challenging task. Ontologies provide a formal framework to support querying and integration. This paper provides an ontology-based solution for querying distributed databases over service-oriented, model-driven infrastructures. PMID:22373043

IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations.

PubMed

Flifla, M J; Garreau, M; Rolland, J P; Coatrieux, J L; Thomas, D

1992-12-01

'IBIS' is a set of computer programs concerned with the processing of electron micrographs, with particular emphasis on the requirements for structural analyses of biological macromolecules. The software is written in FORTRAN 77 and runs on Unix workstations. A description of the various functions and the implementation mode is given. Some examples illustrate the user interface.

General Purpose Data-Driven Monitoring for Space Operations

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

EMMA: a new paradigm in configurable software

DOE PAGES

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

2017-11-23

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

EMMA: A New Paradigm in Configurable Software

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

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

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

EMMA: a new paradigm in configurable software

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

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

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

EMMA: a new paradigm in configurable software

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Indoor Unmanned Airship System Airborne Control Module Design

NASA Astrophysics Data System (ADS)

YongXia, Gao; YiBo, Li

By adopting STC12C5A60S2 SCM as a system control unit, assisted by appropriate software and hardware resources, we complete the airborne control module's design of unmanned airship system. This paper introduces hardware control module's structure, airship-driven composition and software realization. Verified by the China Science and Technology Museum special-shaped airship,this control module can work well.

Architecting for Large Scale Agile Software Development: A Risk-Driven Approach

DTIC Science & Technology

2013-05-01

addressed aspect of scale in agile software development. Practices such as Scrum of Scrums are meant to address orchestration of multiple development...owner, Scrum master) have differing responsibilities from the roles in the existing phase-based waterfall program structures. Such differences may... Scrum . Communication with both internal and external stakeholders must be open and documentation should not be used as a substitute for communication

Funding for Life: When to Spend the Acquisition Pot

DTIC Science & Technology

2010-05-01

Private Military Sector Software Requirements for OA Spiral Development Strategy for Defense Acquisition Research The Software, Hardware...qb=p`elli= Capital Budgeting for the DoD Energy Saving Contracts/DoD Mobile Assets Financing DoD Budget via PPPs Lessons from Private Sector ...the endeavor can, in part, be related to the stability of the aims and contributory components. Economic growth has been driven by globalisation

Applying formal methods and object-oriented analysis to existing flight software

NASA Technical Reports Server (NTRS)

Cheng, Betty H. C.; Auernheimer, Brent

1993-01-01

Correctness is paramount for safety-critical software control systems. Critical software failures in medical radiation treatment, communications, and defense are familiar to the public. The significant quantity of software malfunctions regularly reported to the software engineering community, the laws concerning liability, and a recent NRC Aeronautics and Space Engineering Board report additionally motivate the use of error-reducing and defect detection software development techniques. The benefits of formal methods in requirements driven software development ('forward engineering') is well documented. One advantage of rigorously engineering software is that formal notations are precise, verifiable, and facilitate automated processing. This paper describes the application of formal methods to reverse engineering, where formal specifications are developed for a portion of the shuttle on-orbit digital autopilot (DAP). Three objectives of the project were to: demonstrate the use of formal methods on a shuttle application, facilitate the incorporation and validation of new requirements for the system, and verify the safety-critical properties to be exhibited by the software.

Just-in-time Database-Driven Web Applications

PubMed Central

2003-01-01

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

Evaluation of software maintain ability with open EHR - a comparison of architectures.

PubMed

Atalag, Koray; Yang, Hong Yul; Tempero, Ewan; Warren, James R

2014-11-01

To assess whether it is easier to maintain a clinical information system developed using open EHR model driven development versus mainstream methods. A new open source application (GastrOS) has been developed following open EHR's multi-level modelling approach using .Net/C# based on the same requirements of an existing clinically used application developed using Microsoft Visual Basic and Access database. Almost all the domain knowledge was embedded into the software code and data model in the latter. The same domain knowledge has been expressed as a set of open EHR Archetypes in GastrOS. We then introduced eight real-world change requests that had accumulated during live clinical usage, and implemented these in both systems while measuring time for various development tasks and change in software size for each change request. Overall it took half the time to implement changes in GastrOS. However it was the more difficult application to modify for one change request, suggesting the nature of change is also important. It was not possible to implement changes by modelling only. Comparison of relative measures of time and software size change within each application highlights how architectural differences affected maintain ability across change requests. The use of open EHR model driven development can result in better software maintain ability. The degree to which open EHR affects software maintain ability depends on the extent and nature of domain knowledge involved in changes. Although we used relative measures for time and software size, confounding factors could not be totally excluded as a controlled study design was not feasible. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Practical experience with test-driven development during commissioning of the multi-star AO system ARGOS

NASA Astrophysics Data System (ADS)

Kulas, M.; Borelli, Jose Luis; Gässler, Wolfgang; Peter, Diethard; Rabien, Sebastian; Orban de Xivry, Gilles; Busoni, Lorenzo; Bonaglia, Marco; Mazzoni, Tommaso; Rahmer, Gustavo

2014-07-01

Commissioning time for an instrument at an observatory is precious, especially the night time. Whenever astronomers come up with a software feature request or point out a software defect, the software engineers have the task to find a solution and implement it as fast as possible. In this project phase, the software engineers work under time pressure and stress to deliver a functional instrument control software (ICS). The shortness of development time during commissioning is a constraint for software engineering teams and applies to the ARGOS project as well. The goal of the ARGOS (Advanced Rayleigh guided Ground layer adaptive Optics System) project is the upgrade of the Large Binocular Telescope (LBT) with an adaptive optics (AO) system consisting of six Rayleigh laser guide stars and wavefront sensors. For developing the ICS, we used the technique Test- Driven Development (TDD) whose main rule demands that the programmer writes test code before production code. Thereby, TDD can yield a software system, that grows without defects and eases maintenance. Having applied TDD in a calm and relaxed environment like office and laboratory, the ARGOS team has profited from the benefits of TDD. Before the commissioning, we were worried that the time pressure in that tough project phase would force us to drop TDD because we would spend more time writing test code than it would be worth. Despite this concern at the beginning, we could keep TDD most of the time also in this project phase This report describes the practical application and performance of TDD including its benefits, limitations and problems during the ARGOS commissioning. Furthermore, it covers our experience with pair programming and continuous integration at the telescope.

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

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

PubMed Central

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

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. PMID:25428375

Experimental investigation of nozzle/plume aerodynamics at hypersonic speeds

NASA Technical Reports Server (NTRS)

Bogdanoff, David W.; Cambier, Jean-Luc

1993-01-01

Work continued on the improvement of 16-Inch Shock Tunnel. This comprised studies of ways of improving driver gas ignition, an improved driver gas mixing system, an axial translation system for the driver tube, improved diaphragm materials (carbon steel vs. stainless steel), a copper liner for the part of the driven tube near the nozzle, the use of a buffer gas between the driver and driven gases, the use of N2O in the driven tube, the use of a converging driven tube, operation of the facility as a non-reflected shock tunnel and expansion tube, operation with heated hydrogen or helium driver gas, the use of detonations in the driver and the construction of an enlarged test section. Maintenance and developmental work continued on the scramjet combustor continued. New software which greatly speeds up data analysis has been written and brought on line. In particular, software which provides very rapid generation of model surface heat flux profiles has been brought on line. A considerable amount of theoretical work was performed in connection with upgrading the 16 Inch Shock Tunnel Facility. A one-dimensional Godunov code for very high velocities and any equation of state is intended to add viscous effects in studying the operation of the Shock Tunnel and also of two-stage light gas guns.

A knowledge discovery object model API for Java

PubMed Central

Zuyderduyn, Scott D; Jones, Steven JM

2003-01-01

Background Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized. Results This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually. Conclusions The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at . PMID:14583100

First Steps in Computational Systems Biology: A Practical Session in Metabolic Modeling and Simulation

ERIC Educational Resources Information Center

Reyes-Palomares, Armando; Sanchez-Jimenez, Francisca; Medina, Miguel Angel

2009-01-01

A comprehensive understanding of biological functions requires new systemic perspectives, such as those provided by systems biology. Systems biology approaches are hypothesis-driven and involve iterative rounds of model building, prediction, experimentation, model refinement, and development. Developments in computer science are allowing for ever…

All biology is computational biology.

PubMed

Markowetz, Florian

2017-03-01

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

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

PubMed

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

2016-09-01

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

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

PubMed

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

2017-04-01

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

RAD-ADAPT: Software for modelling clonogenic assay data in radiation biology.

PubMed

Zhang, Yaping; Hu, Kaiqiang; Beumer, Jan H; Bakkenist, Christopher J; D'Argenio, David Z

2017-04-01

We present a comprehensive software program, RAD-ADAPT, for the quantitative analysis of clonogenic assays in radiation biology. Two commonly used models for clonogenic assay analysis, the linear-quadratic model and single-hit multi-target model, are included in the software. RAD-ADAPT uses maximum likelihood estimation method to obtain parameter estimates with the assumption that cell colony count data follow a Poisson distribution. The program has an intuitive interface, generates model prediction plots, tabulates model parameter estimates, and allows automatic statistical comparison of parameters between different groups. The RAD-ADAPT interface is written using the statistical software R and the underlying computations are accomplished by the ADAPT software system for pharmacokinetic/pharmacodynamic systems analysis. The use of RAD-ADAPT is demonstrated using an example that examines the impact of pharmacologic ATM and ATR kinase inhibition on human lung cancer cell line A549 after ionizing radiation. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Wang, Shaowen; Liu, Yan; Padmanabhan, Anand

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

Learning Systems Biology: Conceptual Considerations toward a Web-Based Learning Platform

ERIC Educational Resources Information Center

Emmert-Streib, Frank; Dehmer, Matthias; Lyardet, Fernando

2013-01-01

Within recent years, there is an increasing need to train students, from biology and beyond, in quantitative methods that are relevant to cope with data-driven biology. Systems Biology is such a field that places a particular focus on the functional aspect of biology and molecular interacting processes. This paper deals with the conceptual design…

Simulation of a Canard in Fluid Flow Driven by a Piezoelectric Beam with a Software Control Loop

DTIC Science & Technology

2014-04-01

The canard is actuated by a piezoelectric beam that bends as voltage is applied. The voltage is controlled by a software subroutine that measures...Dynamic system Modeling Co-simulation Simulation Abaqus Finite element analysis (FEA) Finite element method (FEM) Computational...is unlimited. i CONTENTS Page Introduction 1 Model Description 1 Fluid Model 2 Structural Model 3 Control Subroutine 4 Results 4

NPS (Naval Postgraduate School) Supply Requisition Database - Interactive Software as an Alternative to Written Instructions.

DTIC Science & Technology

1986-03-01

SRdb ... .......... .35 APPENDIX A: ABBREVIATIONS AND ACRONYMS ......... 37 " APPENDIX B: USER’S MANUAL ..... ............... 38 APPENDIX C: DATABASE...percentage of situations. The purpose of this paper is to examine and propose a software-oriented alternative to the current manual , instruction-driven...Department Customer Service Manual (Ref. 1] and the applicable NPS Comptroller instruction [Ref. 2]. Several modifications to these written quidelines

Parallel Software Model Checking

DTIC Science & Technology

2015-01-08

checker. This project will explore this strategy to parallelize the generalized PDR algorithm for software model checking. It belongs to TF1 due to its ... focus on formal verification . Generalized PDR. Generalized Property Driven Rechability (GPDR) i is an algorithm for solving HORN-SMT reachability...subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE 08

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.

Qualitative and Quantitative Pedigree Analysis: Graph Theory, Computer Software, and Case Studies.

ERIC Educational Resources Information Center

Jungck, John R.; Soderberg, Patti

1995-01-01

Presents a series of elementary mathematical tools for re-representing pedigrees, pedigree generators, pedigree-driven database management systems, and case studies for exploring genetic relationships. (MKR)

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

PubMed

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

2013-01-01

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

The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va

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

NASA Technical Reports Server (NTRS)

Butler, Roy

2013-01-01

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

Convenience experimentation.

PubMed

Krohs, Ulrich

2012-03-01

Systems biology aims at explaining life processes by means of detailed models of molecular networks, mainly on the whole-cell scale. The whole cell perspective distinguishes the new field of systems biology from earlier approaches within molecular cell biology. The shift was made possible by the high throughput methods that were developed for gathering 'omic' (genomic, proteomic, etc.) data. These new techniques are made commercially available as semi-automatic analytic equipment, ready-made analytic kits and probe arrays. There is a whole industry of supplies for what may be called convenience experimentation. My paper inquires some epistemic consequences of strong reliance on convenience experimentation in systems biology. In times when experimentation was automated to a lesser degree, modeling and in part even experimentation could be understood fairly well as either being driven by hypotheses, and thus proceed by the testing of hypothesis, or as being performed in an exploratory mode, intended to sharpen concepts or initially vague phenomena. In systems biology, the situation is dramatically different. Data collection became so easy (though not cheap) that experimentation is, to a high degree, driven by convenience equipment, and model building is driven by the vast amount of data that is produced by convenience experimentation. This results in a shift in the mode of science. The paper shows that convenience driven science is not primarily hypothesis-testing, nor is it in an exploratory mode. It rather proceeds in a gathering mode. This shift demands another shift in the mode of evaluation, which now becomes an exploratory endeavor, in response to the superabundance of gathered data. Copyright © 2011 Elsevier Ltd. All rights reserved.

Visual Target Tracking on the Mars Exploration Rovers

NASA Technical Reports Server (NTRS)

Kim, Won; Biesiadecki, Jeffrey; Ali, Khaled

2008-01-01

Visual target tracking (VTT) software has been incorporated into Release 9.2 of the Mars Exploration Rover (MER) flight software, now running aboard the rovers Spirit and Opportunity. In the VTT operation (see figure), the rover is driven in short steps between stops and, at each stop, still images are acquired by actively aimed navigation cameras (navcams) on a mast on the rover (see artistic rendition). The VTT software processes the digitized navcam images so as to track a target reliably and to make it possible to approach the target accurately to within a few centimeters over a 10-m traverse.

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

New Software for Ensemble Creation in the Spitzer-Space-Telescope Operations Database

NASA Technical Reports Server (NTRS)

Laher, Russ; Rector, John

2004-01-01

Some of the computer pipelines used to process digital astronomical images from NASA's Spitzer Space Telescope require multiple input images, in order to generate high-level science and calibration products. The images are grouped into ensembles according to well documented ensemble-creation rules by making explicit associations in the operations Informix database at the Spitzer Science Center (SSC). The advantage of this approach is that a simple database query can retrieve the required ensemble of pipeline input images. New and improved software for ensemble creation has been developed. The new software is much faster than the existing software because it uses pre-compiled database stored-procedures written in Informix SPL (SQL programming language). The new software is also more flexible because the ensemble creation rules are now stored in and read from newly defined database tables. This table-driven approach was implemented so that ensemble rules can be inserted, updated, or deleted without modifying software.

MOPEX: a software package for astronomical image processing and visualization

NASA Astrophysics Data System (ADS)

Makovoz, David; Roby, Trey; Khan, Iffat; Booth, Hartley

2006-06-01

We present MOPEX - a software package for astronomical image processing and display. The package is a combination of command-line driven image processing software written in C/C++ with a Java-based GUI. The main image processing capabilities include creating mosaic images, image registration, background matching, point source extraction, as well as a number of minor image processing tasks. The combination of the image processing and display capabilities allows for much more intuitive and efficient way of performing image processing. The GUI allows for the control over the image processing and display to be closely intertwined. Parameter setting, validation, and specific processing options are entered by the user through a set of intuitive dialog boxes. Visualization feeds back into further processing by providing a prompt feedback of the processing results. The GUI also allows for further analysis by accessing and displaying data from existing image and catalog servers using a virtual observatory approach. Even though originally designed for the Spitzer Space Telescope mission, a lot of functionalities are of general usefulness and can be used for working with existing astronomical data and for new missions. The software used in the package has undergone intensive testing and benefited greatly from effective software reuse. The visualization part has been used for observation planning for both the Spitzer and Herschel Space Telescopes as part the tool Spot. The visualization capabilities of Spot have been enhanced and integrated with the image processing functionality of the command-line driven MOPEX. The image processing software is used in the Spitzer automated pipeline processing, which has been in operation for nearly 3 years. The image processing capabilities have also been tested in off-line processing by numerous astronomers at various institutions around the world. The package is multi-platform and includes automatic update capabilities. The software package has been developed by a small group of software developers and scientists at the Spitzer Science Center. It is available for distribution at the Spitzer Science Center web page.

CFEL-ASG Software Suite (CASS): usage for free-electron laser experiments with biological focus.

PubMed

Foucar, Lutz

2016-08-01

CASS [Foucar et al. (2012). Comput. Phys. Commun. 183 , 2207-2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.

The Human Genome Project: Information access, management, and regulation. Final report

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

McInerney, J.D.; Micikas, L.B.

The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

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

PubMed Central

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

2015-01-01

Evaporation is a ubiquitous phenomenon in the natural environment and a dominant form of energy transfer in the Earth's climate. Engineered systems rarely, if ever, use evaporation as a source of energy, despite myriad examples of such adaptations in the biological world. Here, we report evaporation-driven engines that can power common tasks like locomotion and electricity generation. These engines start and run autonomously when placed at air–water interfaces. They generate rotary and piston-like linear motion using specially designed, biologically based artificial muscles responsive to moisture fluctuations. Using these engines, we demonstrate an electricity generator that rests on water while harvesting its evaporation to power a light source, and a miniature car (weighing 0.1 kg) that moves forward as the water in the car evaporates. Evaporation-driven engines may find applications in powering robotic systems, sensors, devices and machinery that function in the natural environment. PMID:26079632

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

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

Visualizing time-related data in biology, a review

PubMed Central

Secrier, Maria; Schneider, Reinhard

2014-01-01

Time is of the essence in biology as in so much else. For example, monitoring disease progression or the timing of developmental defects is important for the processes of drug discovery and therapy trials. Furthermore, an understanding of the basic dynamics of biological phenomena that are often strictly time regulated (e.g. circadian rhythms) is needed to make accurate inferences about the evolution of biological processes. Recent advances in technologies have enabled us to measure timing effects more accurately and in more detail. This has driven related advances in visualization and analysis tools that try to effectively exploit this data. Beyond timeline plots, notable attempts at more involved temporal interpretation have been made in recent years, but awareness of the available resources is still limited within the scientific community. Here, we review some advances in biological visualization of time-driven processes and consider how they aid data analysis and interpretation. PMID:23585583

Position of Curiosity for Drilling at Cumberland

NASA Image and Video Library

2013-06-05

This image produced from software used for planning drives of NASA Mars rover Curiosity depicts the location and size of the rover when it was driven into position for drilling into rock target Cumberland.

A High School-Collegiate Outreach Program in Chemistry and Biology Delivering Modern Technology in a Mobile Van

NASA Astrophysics Data System (ADS)

Craney, Chris; Mazzeo, April; Lord, Kaye

1996-07-01

During the past five years the nation's concern for science education has expanded from a discussion about the future supply of Ph.D. scientists and its impact on the nation's scientific competitiveness to the broader consideration of the science education available to all students. Efforts to improve science education have led many authors to suggest greater collaboration between high school science teachers and their college/university colleagues. This article reviews the experience and outcomes of the Teachers + Occidental = Partnership in Science (TOPS) van program operating in the Los Angeles Metropolitan area. The program emphasizes an extensive ongoing staff development, responsiveness to teachers' concerns, technical and on-site support, and sustained interaction between participants and program staff. Access to modern technology, including computer-driven instruments and commercial data analysis software, coupled with increased teacher content knowledge has led to empowerment of teachers and changes in student interest in science. Results of student and teacher questionnaires are reviewed.

PatternLab for proteomics 4.0: A one-stop shop for analyzing shotgun proteomic data

PubMed Central

Carvalho, Paulo C; Lima, Diogo B; Leprevost, Felipe V; Santos, Marlon D M; Fischer, Juliana S G; Aquino, Priscila F; Moresco, James J; Yates, John R; Barbosa, Valmir C

2017-01-01

PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for analyzing shotgun proteomic data. PatternLab contains modules for formatting sequence databases, performing peptide spectrum matching, statistically filtering and organizing shotgun proteomic data, extracting quantitative information from label-free and chemically labeled data, performing statistics for differential proteomics, displaying results in a variety of graphical formats, performing similarity-driven studies with de novo sequencing data, analyzing time-course experiments, and helping with the understanding of the biological significance of data in the light of the Gene Ontology. Here we describe PatternLab for proteomics 4.0, which closely knits together all of these modules in a self-contained environment, covering the principal aspects of proteomic data analysis as a freely available and easily installable software package. All updates to PatternLab, as well as all new features added to it, have been tested over the years on millions of mass spectra. PMID:26658470

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

PubMed

Bielejec, Filip; Baele, Guy; Vrancken, Bram; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2016-08-01

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

TreSpEx—Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

PubMed Central

Struck, Torsten H

2014-01-01

Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. The program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available at http://www.annelida.de/research/bioinformatics/software.html. PMID:24701118

Integrated multidisciplinary analysis tool IMAT users' guide

NASA Technical Reports Server (NTRS)

Meissner, Frances T. (Editor)

1988-01-01

The Integrated Multidisciplinary Analysis Tool (IMAT) is a computer software system developed at Langley Research Center. IMAT provides researchers and analysts with an efficient capability to analyze satellite controls systems influenced by structural dynamics. Using a menu-driven executive system, IMAT leads the user through the program options. IMAT links a relational database manager to commercial and in-house structural and controls analysis codes. This paper describes the IMAT software system and how to use it.

CrossTalk: The Journal of Defense Software Engineering. Volume 19, Number 9

DTIC Science & Technology

2006-09-01

it does. Several freely down- loadable methodologies have emerged to support the developer in modeling threats to applications and other soft...SECURIS. Model -Driven Develop - ment and Analysis of Secure Information Systems <www.sintef.no/ content/page1_1824.aspx>. 10. The SECURIS Project ...By applying these methods to the SDLC , we can actively reduce the number of known vulnerabilities in software as it is developed . For

Are Earth System model software engineering practices fit for purpose? A case study.

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.; Johns, T. C.

2009-04-01

We present some analysis and conclusions from a case study of the culture and practices of scientists at the Met Office and Hadley Centre working on the development of software for climate and Earth System models using the MetUM infrastructure. The study examined how scientists think about software correctness, prioritize their requirements in making changes, and develop a shared understanding of the resulting models. We conclude that highly customized techniques driven strongly by scientific research goals have evolved for verification and validation of such models. In a formal software engineering context these represents costly, but invaluable, software integration tests with considerable benefits. The software engineering practices seen also exhibit recognisable features of both agile and open source software development projects - self-organisation of teams consistent with a meritocracy rather than top-down organisation, extensive use of informal communication channels, and software developers who are generally also users and science domain experts. We draw some general conclusions on whether these practices work well, and what new software engineering challenges may lie ahead as Earth System models become ever more complex and petascale computing becomes the norm.

NDEx - the Network Data Exchange, A Network Commons for Biologists | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Network models of biology, whether curated or derived from large-scale data analysis, are critical tools in the understanding of cancer mechanisms and in the design and personalization of therapies. The NDEx Project (Network Data Exchange) will create, deploy, and maintain an open-source, web-based software platform and public website to enable scientists, organizations, and software applications to share, store, manipulate, and publish biological networks.

JBEI Registry

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

Ham, Timothy

2008-12-01

The JBEI Registry is a software to store and manage to a database of biological parts. It is intended to be used as a web service that is accessed via a web browser. It is also capable of running as a desktop program for a single user. The registry software stores, indexes, categories, and allows users to enter, search, retrieve, and contruct biological constructs in silico. It is also able to communicate with other Registries for data sharing and exchange.

A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source

PubMed Central

Breitkopf, Susanne B.; Ricoult, Stéphane J. H.; Yuan, Min; Xu, Ying; Peake, David A.; Manning, Brendan D.

2017-01-01

Introduction Advances in high-resolution mass spectrometry have created renewed interest for studying global lipid biochemistry in disease and biological systems. Objectives Here, we present an untargeted 30 min. LC-MS/MS platform that utilizes positive/negative polarity switching to perform unbiased data dependent acquisitions (DDA) via higher energy collisional dissociation (HCD) fragmentation to profile more than 1000–1500 lipid ions mainly from methyl-tert-butyl ether (MTBE) or chloroform:methanol extractions. Methods The platform uses C18 reversed-phase chromatography coupled to a hybrid QExactive Plus/HF Orbitrap mass spectrometer and the entire procedure takes ~10 h from lipid extraction to identification/quantification for a data set containing 12 samples (~4 h for a single sample). Lipids are identified by both accurate precursor ion mass and fragmentation features and quantified using Lipid-Search and Elements software. Results Using this approach, we are able to profile intact lipid ions from up to 18 different main lipid classes and 66 subclasses. We show several studies from different biological sources, including cultured cancer cells, resected tissues from mice such as lung and breast tumors and biological fluids such as plasma and urine. Conclusions Using mouse embryonic fibroblasts, we showed that TSC2−/− KD significantly abrogates lipid biosynthesis and that rapamycin can rescue triglyceride (TG) lipids and we show that SREBP−/− shuts down lipid biosynthesis significantly via mTORC1 signaling pathways. We show that in mouse EGFR driven lung tumors, a large number of TGs and phosphatidylmethanol (PMe) lipids are elevated while some phospholipids (PLs) show some of the largest decrease in lipid levels from ~ 2000 identified lipid ions. In addition, we identified more than 1500 unique lipid species from human blood plasma. PMID:28496395

Dependability modeling and assessment in UML-based software development.

PubMed

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

2012-01-01

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

Dependability Modeling and Assessment in UML-Based Software Development

PubMed Central

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

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results. PMID:22988428

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

NASA Technical Reports Server (NTRS)

Tischer, A. E.

1987-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

PubMed

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Educational Software Evaluation Form for Teachers

ERIC Educational Resources Information Center

Kara, Yilmaz

2007-01-01

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

From Presentation to Programming: Doing Something Different, Not the Same Thing Differently.

ERIC Educational Resources Information Center

Galas, Cathleen

1998-01-01

Discusses the use of multimedia software and the need to apply constructivist theories so students become more involved with the software, progressing from simply watching presentations to creating simulations. A project-based learning environment that uses MicroWorlds software is described that focuses on marine biology and oceanography. (LRW)

Science Laboratory Depth of Learning: Interactive Multimedia Simulation and Virtual Dissection Software

ERIC Educational Resources Information Center

Yuza, Steve C.

2010-01-01

The purpose of this study was to determine the effects of interactive multimedia simulations and virtual dissection software on depth of learning among students participating in biology and chemistry laboratory courses. By understanding more about how simulation and virtual dissection software changes depth of learning, educators will have the…

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

PubMed

Stein, Lincoln D

2008-09-01

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

Light-energy conversion in engineered microorganisms.

PubMed

Johnson, Ethan T; Schmidt-Dannert, Claudia

2008-12-01

Increasing interest in renewable resources by the energy and chemical industries has spurred new technologies both to capture solar energy and to develop biologically derived chemical feedstocks and fuels. Advances in molecular biology and metabolic engineering have provided new insights and techniques for increasing biomass and biohydrogen production, and recent efforts in synthetic biology have demonstrated that complex regulatory and metabolic networks can be designed and engineered in microorganisms. Here, we explore how light-driven processes may be incorporated into nonphotosynthetic microbes to boost metabolic capacity for the production of industrial and fine chemicals. Progress towards the introduction of light-driven proton pumping or anoxygenic photosynthesis into Escherichia coli to increase the efficiency of metabolically-engineered biosynthetic pathways is highlighted.

Textual data compression in computational biology: a synopsis.

PubMed

Giancarlo, Raffaele; Scaturro, Davide; Utro, Filippo

2009-07-01

Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been used. When possible, a unifying organization of the main ideas and techniques is also provided. It goes without saying that most of the research results reviewed here offer software prototypes to the bioinformatics community. The Supplementary Material provides pointers to software and benchmark datasets for a range of applications of broad interest. In addition to provide reference to software, the Supplementary Material also gives a brief presentation of some fundamental results and techniques related to this paper. It is at: http://www.math.unipa.it/ approximately raffaele/suppMaterial/compReview/

A metadata-driven approach to data repository design.

PubMed

Harvey, Matthew J; McLean, Andrew; Rzepa, Henry S

2017-01-01

The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with DataCite in accordance with their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data preview are illustrated, including the demonstration of a method for integration with commercial software that confers rich domain-specific data analytics without introducing customisation into the repository itself.

Radiobiological study by using laser-driven proton beams

NASA Astrophysics Data System (ADS)

Yogo, A.; Sato, K.; Nishikino, M.; Mori, M.; Teshima, T.; Numasaki, H.; Murakami, M.; Demizu, Y.; Akagi, S.; Nagayama, S.; Ogura, K.; Sagisaka, A.; Orimo, S.; Nishiuchi, M.; Pirozhkov, A. S.; Ikegami, M.; Tampo, M.; Sakaki, H.; Suzuki, M.; Daito, I.; Oishi, Y.; Sugiyama, H.; Kiriyama, H.; Okada, H.; Kanazawa, S.; Kondo, S.; Shimomura, T.; Nakai, Y.; Tanoue, M.; Sugiyama, H.; Sasao, H.; Wakai, D.; Kawachi, T.; Nishimura, H.; Bolton, P. R.; Daido, H.

2009-07-01

Particle acceleration driven by high-intensity laser systems is widely attracting interest as a potential alternative to conventional ion acceleration, including ion accelerator applications to tumor therapy. Recent works have shown that a high intensity laser pulse can produce single proton bunches of a high current and a short pulse duration. This unique feature of laser-ion acceleration can lead to progress in the development of novel ion sources. However, there has been no experimental study of the biological effects of laser-driven ion beams. We describe in this report the first demonstrated irradiation effect of laser-accelerated protons on human lung cancer cells. In-vitro A549 cells are irradiated with a proton dose of 20 Gy, resulting in a distinct formation of γ-H2AX foci as an indicator of DNA double-strand breaks. This is a pioneering result that points to future investigations of the radiobiological effects of laser-driven ion beams. The laser-driven ion beam is apotential excitation source for time-resolved determination of hydroxyl (OH) radical yield, which will explore relationship between the fundamental chemical reactions of radiation effects and consequent biological processes.

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

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

Hadley, S; Kessler, M; Litzenberg, D

2015-06-15

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

Shaping biological knowledge: applications in proteomics.

PubMed

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

2004-01-01

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

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

Dissecting the COW

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

Linstadt, E.

1985-10-01

The COW, or Console On Wheels, is the primary operator interface to the SLC accelerator control system. A hardware and software description of the COW, a microcomputer based system with a color graphics display output and touchpanel and knob inputs, is given. The ease of development and expandability, due to both the modular nature of the hardware and the multitasking, interrupt driven software running in the COW, are described. Integration of the COW into the SLCNET communications network and SLC Control system is detailed.

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

PubMed

Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

2016-09-02

Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNP(xl) for UV-induced peptide-RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark ( Ramus, C.; J. Proteomics 2016 , 132 , 51 - 62 ). The second workflow, RNP(xl), represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

The Case for "Story-Driven" Biology Education

ERIC Educational Resources Information Center

Schattner, Peter

2015-01-01

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

Software Reviews.

ERIC Educational Resources Information Center

Science Software Quarterly, 1984

1984-01-01

Provides extensive reviews of computer software, examining documentation, ease of use, performance, error handling, special features, and system requirements. Includes statistics, problem-solving (TK Solver), label printing, database management, experimental psychology, Encyclopedia Britannica biology, and DNA-sequencing programs. A program for…

Computer Center: Software Review.

ERIC Educational Resources Information Center

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

1988-01-01

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

GRAPHICS MANAGER (GFXMGR): An interactive graphics software program for the Advanced Electronics Design (AED) graphics controller, Model 767

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

Faculjak, D.A.

1988-03-01

Graphics Manager (GFXMGR) is menu-driven, user-friendly software designed to interactively create, edit, and delete graphics displays on the Advanced Electronics Design (AED) graphics controller, Model 767. The software runs on the VAX family of computers and has been used successfully in security applications to create and change site layouts (maps) of specific facilities. GFXMGR greatly benefits graphics development by minimizing display-development time, reducing tedium on the part of the user, and improving system performance. It is anticipated that GFXMGR can be used to create graphics displays for many types of applications. 8 figs., 2 tabs.

End-to-end observatory software modeling using domain specific languages

NASA Astrophysics Data System (ADS)

Filgueira, José M.; Bec, Matthieu; Liu, Ning; Peng, Chien; Soto, José

2014-07-01

The Giant Magellan Telescope (GMT) is a 25-meter extremely large telescope that is being built by an international consortium of universities and research institutions. Its software and control system is being developed using a set of Domain Specific Languages (DSL) that supports a model driven development methodology integrated with an Agile management process. This approach promotes the use of standardized models that capture the component architecture of the system, that facilitate the construction of technical specifications in a uniform way, that facilitate communication between developers and domain experts and that provide a framework to ensure the successful integration of the software subsystems developed by the GMT partner institutions.

Composable Framework Support for Software-FMEA Through Model Execution

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

The look of LaTeX

NASA Astrophysics Data System (ADS)

This has always been the major objection to its use by those not driven by the need to typeset mathematics since the “what-you-see-is-what-you-get” (WYSIWYG) packages offered by Microsoft Word and WordPerfect are easy to learn and use. Recently, however, com-mercial software companies have begun to market almost-WYSIWYG programs that create LaTeX files. Some commercial software that creates LaTeX files are listed in Table 1. EXP and SWP have some of the “look and feel” of the software that is popular in offices and PCTeX32 allows quick and convenient previews of the translated LaTeX files.

Evolving Strategies for the Incorporation of Bioinformatics within the Undergraduate Cell Biology Curriculum

ERIC Educational Resources Information Center

Honts, Jerry E.

2003-01-01

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in…

Road embankment and slope stabilization.

DOT National Transportation Integrated Search

2010-07-31

This report and the accompanying software are part of efforts to improve the characterization and analysis of pilestabilized : slopes using one or two rows of driven piles. A combination of the limit equilibrium analysis and strain : wedge (SW) model...

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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

NASA Technical Reports Server (NTRS)

Izygon, Michel E.

1992-01-01

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

Preliminary Dynamic Feasibility and Analysis of a Spherical, Wind-Driven (Tumbleweed), Martian Rover

NASA Technical Reports Server (NTRS)

Flick, John J.; Toniolo, Matthew D.

2005-01-01

The process and findings are presented from a preliminary feasibility study examining the dynamics characteristics of a spherical wind-driven (or Tumbleweed) rover, which is intended for exploration of the Martian surface. The results of an initial feasibility study involving several worst-case mobility situations that a Tumbleweed rover might encounter on the surface of Mars are discussed. Additional topics include the evaluation of several commercially available analysis software packages that were examined as possible platforms for the development of a Monte Carlo Tumbleweed mission simulation tool. This evaluation lead to the development of the Mars Tumbleweed Monte Carlo Simulator (or Tumbleweed Simulator) using the Vortex physics software package from CM-Labs, Inc. Discussions regarding the development and evaluation of the Tumbleweed Simulator, as well as the results of a preliminary analysis using the tool are also presented. Finally, a brief conclusions section is presented.

Consistent model driven architecture

NASA Astrophysics Data System (ADS)

Niepostyn, Stanisław J.

2015-09-01

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

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

PubMed

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

2010-09-15

The decision peptide-driven tool implements a software application for assisting the user in a protocol for accurate protein quantification based on the following steps: (1) protein separation through gel electrophoresis; (2) in-gel protein digestion; (3) direct and inverse (18)O-labeling and (4) matrix assisted laser desorption ionization time of flight mass spectrometry, MALDI analysis. The DPD software compares the MALDI results of the direct and inverse (18)O-labeling experiments and quickly identifies those peptides with paralleled loses in different sets of a typical proteomic workflow. Those peptides are used for subsequent accurate protein quantification. The interpretation of the MALDI data from direct and inverse labeling experiments is time-consuming requiring a significant amount of time to do all comparisons manually. The DPD software shortens and simplifies the searching of the peptides that must be used for quantification from a week to just some minutes. To do so, it takes as input several MALDI spectra and aids the researcher in an automatic mode (i) to compare data from direct and inverse (18)O-labeling experiments, calculating the corresponding ratios to determine those peptides with paralleled losses throughout different sets of experiments; and (ii) allow to use those peptides as internal standards for subsequent accurate protein quantification using (18)O-labeling. In this work the DPD software is presented and explained with the quantification of protein carbonic anhydrase. Copyright (c) 2010 Elsevier B.V. All rights reserved.

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.

Does the transition to an active-learning environment for the introductory course reduce students' overall knowledge of the various disciplines in biology?

PubMed

Simurda, Maryanne C

2012-01-01

As biology education is being redesigned toward an interdisciplinary focus and as pedagogical trends move toward active-learning strategies and investigative experiences, a restructuring of the course content for the Introductory Biology course is necessary. The introductory course in biology has typically been a survey of all the biosciences. If the total number of topics covered is reduced, is the students' overall knowledge of biology also reduced? Our introductory course has been substantially modified away from surveying the biological sciences and toward providing a deep understanding of a particular biological topic, as well as focusing on developing students' analytical and communication skills. Because of this shift to a topic-driven approach for the introductory course, we were interested in assessing our graduating students' overall knowledge of the various biological disciplines. Using the Major Field Test - Biology (Educational Testing Service (ETS), Princeton, NJ), we compared the test performance of graduating students who had a traditional lecture-based introductory course to those who had a topic-driven active-learning introductory course. Our results suggest that eliminating the traditional survey of biology and, instead, focusing on quantitative and writing skills at the introductory level do not affect our graduating students' overall breadth of knowledge of the various biosciences.

Biological Inquiry: A New Course and Assessment Plan in Response to the Call to Transform Undergraduate Biology

ERIC Educational Resources Information Center

Goldey, Ellen S.; Abercrombie, Clarence L.; Ivy, Tracie M.; Kusher, Dave I.; Moeller, John F.; Rayner, Doug A.; Smith, Charles F.; Spivey, Natalie W.

2012-01-01

We transformed our first-year curriculum in biology with a new course, Biological Inquiry, in which greater than 50% of all incoming, first-year students enroll. The course replaced a traditional, content-driven course that relied on outdated approaches to teaching and learning. We diversified pedagogical practices by adopting guided inquiry in…

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.

PubMed

Sen Sarma, Moushumi; Arcoleo, David; Khetani, Radhika S; Chee, Brant; Ling, Xu; He, Xin; Jiang, Jing; Mei, Qiaozhu; Zhai, ChengXiang; Schatz, Bruce

2011-07-01

With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at www.beespace.illinois.edu for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available at www.beespace.illinois.edu/bstwmaterials.php.

Achieving reutilization of scheduling software through abstraction and generalization

NASA Technical Reports Server (NTRS)

Wilkinson, George J.; Monteleone, Richard A.; Weinstein, Stuart M.; Mohler, Michael G.; Zoch, David R.; Tong, G. Michael

1995-01-01

Reutilization of software is a difficult goal to achieve particularly in complex environments that require advanced software systems. The Request-Oriented Scheduling Engine (ROSE) was developed to create a reusable scheduling system for the diverse scheduling needs of the National Aeronautics and Space Administration (NASA). ROSE is a data-driven scheduler that accepts inputs such as user activities, available resources, timing contraints, and user-defined events, and then produces a conflict-free schedule. To support reutilization, ROSE is designed to be flexible, extensible, and portable. With these design features, applying ROSE to a new scheduling application does not require changing the core scheduling engine, even if the new application requires significantly larger or smaller data sets, customized scheduling algorithms, or software portability. This paper includes a ROSE scheduling system description emphasizing its general-purpose features, reutilization techniques, and tasks for which ROSE reuse provided a low-risk solution with significant cost savings and reduced software development time.

A Spiking Neural Simulator Integrating Event-Driven and Time-Driven Computation Schemes Using Parallel CPU-GPU Co-Processing: A Case Study.

PubMed

Naveros, Francisco; Luque, Niceto R; Garrido, Jesús A; Carrillo, Richard R; Anguita, Mancia; Ros, Eduardo

2015-07-01

Time-driven simulation methods in traditional CPU architectures perform well and precisely when simulating small-scale spiking neural networks. Nevertheless, they still have drawbacks when simulating large-scale systems. Conversely, event-driven simulation methods in CPUs and time-driven simulation methods in graphic processing units (GPUs) can outperform CPU time-driven methods under certain conditions. With this performance improvement in mind, we have developed an event-and-time-driven spiking neural network simulator suitable for a hybrid CPU-GPU platform. Our neural simulator is able to efficiently simulate bio-inspired spiking neural networks consisting of different neural models, which can be distributed heterogeneously in both small layers and large layers or subsystems. For the sake of efficiency, the low-activity parts of the neural network can be simulated in CPU using event-driven methods while the high-activity subsystems can be simulated in either CPU (a few neurons) or GPU (thousands or millions of neurons) using time-driven methods. In this brief, we have undertaken a comparative study of these different simulation methods. For benchmarking the different simulation methods and platforms, we have used a cerebellar-inspired neural-network model consisting of a very dense granular layer and a Purkinje layer with a smaller number of cells (according to biological ratios). Thus, this cerebellar-like network includes a dense diverging neural layer (increasing the dimensionality of its internal representation and sparse coding) and a converging neural layer (integration) similar to many other biologically inspired and also artificial neural networks.

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

Reviews five software packages for use with school age children. Includes "Science Toolkit Module 2: Earthquake Lab"; "Adaptations and Identification"; "Geoworld"; "Body Systems II Series: The Blood System: A Liquid of Life," all for Apple II, and "Science Courseware: Life Science/Biology" for…

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

DOE PAGES

Chen, Xi; Goodnight, Davis; Gao, Zhenghan; ...

2015-06-16

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

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

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

Chen, Xi; Goodnight, Davis; Gao, Zhenghan

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

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

PubMed Central

Gogoshin, Grigoriy; Boerwinkle, Eric

2017-01-01

Abstract Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs. To overcome these and other obstacles, we present BNOmics, an improved algorithm and software toolkit for inferring and analyzing BNs from omics datasets. BNOmics aims at comprehensive systems biology—type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Novel aspects of the algorithm center around increasing scalability and applicability to varying data types (with different explicit and implicit distributional assumptions) within the same analysis framework. An output and visualization interface to widely available graph-rendering software is also included. Three diverse applications are detailed. BNOmics was originally developed in the context of genetic epidemiology data and is being continuously optimized to keep pace with the ever-increasing inflow of available large-scale omics datasets. As such, the software scalability and usability on the less than exotic computer hardware are a priority, as well as the applicability of the algorithm and software to the heterogeneous datasets containing many data types—single-nucleotide polymorphisms and other genetic/epigenetic/transcriptome variables, metabolite levels, epidemiological variables, endpoints, and phenotypes, etc. PMID:27681505

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

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849

Software-Reconfigurable Processors for Spacecraft

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

AN AUTOMATED MONITORING SYSTEM FOR FISH PHYSIOLOGY AND TOXICOLOGY

EPA Science Inventory

This report describes a data acquisition and control (DAC) system that was constructed to manage selected physiological measurements and sample control for aquatic physiology and toxicology. Automated DAC was accomplished with a microcomputer running menu-driven software develope...

Dissecting the COW

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

Linstadt, E.

1985-04-01

The COW, or Console On Wheels, is the primary operator interface to the SLC accelerator control system. A hardware and software description of the COW, a microcomputer based system with a color graphics display output and touch-panel and knob inputs, is given. The ease of development and expandability, due to both the modular nature of the hardware and the multitasking, interrupt driven software running in the COW, are described. Integration of the COW into the SLCNET communications network and SLC Control system is detailed.

Software Product Lines: Report of the 2009 U.S. Army Software Product Line Workshop

DTIC Science & Technology

2009-04-01

record system was fielded in 2008. One early challenge for Overwatch was coming up with a funding model that would support core asset development (a...match the organizational model to the funding model . Product line architecture is essential. Address product line requirements up front. Put processes...when trying to move from a customer-driven, product-specific funding model to one in which at least some of the funds are allocated to the creation and

Program Aids Design Of Fluid-Circulating Systems

NASA Technical Reports Server (NTRS)

Bacskay, Allen; Dalee, Robert

1992-01-01

Computer Aided Systems Engineering and Analysis (CASE/A) program is interactive software tool for trade study and analysis, designed to increase productivity during all phases of systems engineering. Graphics-based command-driven software package provides user-friendly computing environment in which engineer analyzes performance and interface characteristics of ECLS/ATC system. Useful during all phases of spacecraft-design program, from initial conceptual design trade studies to actual flight, including pre-flight prediction and in-flight analysis of anomalies. Written in FORTRAN 77.

IMAT (Integrated Multidisciplinary Analysis Tool) user's guide for the VAX/VMS computer

NASA Technical Reports Server (NTRS)

Meissner, Frances T. (Editor)

1988-01-01

The Integrated Multidisciplinary Analysis Tool (IMAT) is a computer software system for the VAX/VMS computer developed at the Langley Research Center. IMAT provides researchers and analysts with an efficient capability to analyze satellite control systems influenced by structural dynamics. Using a menu-driven executive system, IMAT leads the user through the program options. IMAT links a relational database manager to commercial and in-house structural and controls analysis codes. This paper describes the IMAT software system and how to use it.

From the Director: The Joy of Science, the Courage of Research

MedlinePlus

... Dr. Zerhouni , one that combines an appreciation of biological complexity with the fearless search for scientific knowledge. ... techniques for greater understanding of the complexity of biological systems. The one thing that has driven my ...

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

PubMed

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

2015-08-14

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

Browndye: A Software Package for Brownian Dynamics

PubMed Central

McCammon, J. Andrew

2010-01-01

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. PMID:21132109

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.

PubMed

Sauro, Herbert M; Hucka, Michael; Finney, Andrew; Wellock, Cameron; Bolouri, Hamid; Doyle, John; Kitano, Hiroaki

2003-01-01

Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.

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.

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

PubMed

Trivedi, Prinal; Edwards, Jode W; Wang, Jelai; Gadbury, Gary L; Srinivasasainagendra, Vinodh; Zakharkin, Stanislav O; Kim, Kyoungmi; Mehta, Tapan; Brand, Jacob P L; Patki, Amit; Page, Grier P; Allison, David B

2005-04-06

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

Software Certification - Coding, Code, and Coders

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Holzmann, Gerard J.

2011-01-01

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

Identifying biologically relevant differences between metagenomic communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2010-03-15

Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis. We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport. Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP CONTACT: beiko@cs.dal.ca Supplementary data are available at Bioinformatics online.

Molecular mechanics and dynamics characterization of an in silico mutated protein: a stand-alone lab module or support activity for in vivo and in vitro analyses of targeted proteins.

PubMed

Chiang, Harry; Robinson, Lucy C; Brame, Cynthia J; Messina, Troy C

2013-01-01

Over the past 20 years, the biological sciences have increasingly incorporated chemistry, physics, computer science, and mathematics to aid in the development and use of mathematical models. Such combined approaches have been used to address problems from protein structure-function relationships to the workings of complex biological systems. Computer simulations of molecular events can now be accomplished quickly and with standard computer technology. Also, simulation software is freely available for most computing platforms, and online support for the novice user is ample. We have therefore created a molecular dynamics laboratory module to enhance undergraduate student understanding of molecular events underlying organismal phenotype. This module builds on a previously described project in which students use site-directed mutagenesis to investigate functions of conserved sequence features in members of a eukaryotic protein kinase family. In this report, we detail the laboratory activities of a MD module that provide a complement to phenotypic outcomes by providing a hypothesis-driven and quantifiable measure of predicted structural changes caused by targeted mutations. We also present examples of analyses students may perform. These laboratory activities can be integrated with genetics or biochemistry experiments as described, but could also be used independently in any course that would benefit from a quantitative approach to protein structure-function relationships. Copyright © 2013 Wiley Periodicals, Inc.

National Center for Biotechnology Information Celebrates 25th Anniversary | NIH MedlinePlus the Magazine

MedlinePlus

... is a national and international resource for molecular biology information. It creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and ...

Reviews.

ERIC Educational Resources Information Center

Science Teacher, 1989

1989-01-01

Reviews seven software programs: (1) "Science Baseball: Biology" (testing a variety of topics); (2) "Wildways: Understanding Wildlife Conservation"; (3) "Earth Science Computer Test Bank"; (4) "Biology Computer Test Bank"; (5) "Computer Play & Learn Series" (a series of drill and test…

College Students' Misconceptions about Evolutionary Trees

ERIC Educational Resources Information Center

Meir, Eli; Perry, Judy; Herron, Jon C.; Kingsolver, Joel

2007-01-01

Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and…

Open Source Next Generation Visualization Software for Interplanetary Missions

NASA Technical Reports Server (NTRS)

Trimble, Jay; Rinker, George

2016-01-01

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

The Future of Data Reduction at UKIRT

NASA Astrophysics Data System (ADS)

Economou, F.; Bridger, A.; Wright, G. S.; Rees, N. P.; Jenness, T.

The Observatory Reduction and Acquisition Control (ORAC) project is a comprehensive re-implementation of all existing instrument user interfaces and data handling software involved at the United Kingdom Infrared Telescope (UKIRT). This paper addresses the design of the data reduction part of the system. Our main aim is to provide data reduction facilities for the new generation of UKIRT instruments of a similar standard to our current software packages, which have enjoyed success because of their science-driven approach. Additionally we wish to use modern software techniques in order to produce a system that is portable, flexible and extensible so as to have modest maintenance requirements, both in the medium and the longer term.

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

PubMed

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

2013-12-01

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

A Data-Driven Solution for Performance Improvement

NASA Technical Reports Server (NTRS)

2002-01-01

Marketed as the "Software of the Future," Optimal Engineering Systems P.I. EXPERT(TM) technology offers statistical process control and optimization techniques that are critical to businesses looking to restructure or accelerate operations in order to gain a competitive edge. Kennedy Space Center granted Optimal Engineering Systems the funding and aid necessary to develop a prototype of the process monitoring and improvement software. Completion of this prototype demonstrated that it was possible to integrate traditional statistical quality assurance tools with robust optimization techniques in a user- friendly format that is visually compelling. Using an expert system knowledge base, the software allows the user to determine objectives, capture constraints and out-of-control processes, predict results, and compute optimal process settings.

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

ERIC Educational Resources Information Center

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

2004-01-01

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

Collecting, Integrating, and Disseminating Patient-Reported Outcomes for Research in a Learning Healthcare System

PubMed Central

Harle, Christopher A.; Lipori, Gloria; Hurley, Robert W.

2016-01-01

Introduction: Advances in health policy, research, and information technology have converged to increase the electronic collection and use of patient-reported outcomes (PROs). Therefore, it is important to share lessons learned in implementing PROs in research information systems. Case Description: The purpose of this case study is to describe a novel information system for electronic PROs and lessons learned in implementing that system to support research in an academic health center. The system incorporates freely available and commercial software and involves clinical and research workflows that support the collection, transformation, and research use of PRO data. The software and processes that comprise the system serve three main functions, (i) collecting electronic PROs in clinical care, (ii) integrating PRO data with non-patient generated clinical data, and (iii) disseminating data to researchers through the institution’s research informatics infrastructure, including the i2b2 (Informatics for Integrating Biology and the Bedside) system. Strategies: Our successful design and implementation was driven by three overarching strategies. First, we selected and implemented multiple interfaced technologies to support PRO collection, management, and research use. Second, we aimed to use standardized approaches to measuring PROs, sending PROs between systems, and disseminating PROs. Finally, we focused on using technologies and processes that aligned with existing clinical research information management strategies within our organization. Conclusion: These experiences and lessons may help future implementers and researchers enhance the scale and sustainable use of systems for research use of PROs. PMID:27563683

Collecting, Integrating, and Disseminating Patient-Reported Outcomes for Research in a Learning Healthcare System.

PubMed

Harle, Christopher A; Lipori, Gloria; Hurley, Robert W

2016-01-01

Advances in health policy, research, and information technology have converged to increase the electronic collection and use of patient-reported outcomes (PROs). Therefore, it is important to share lessons learned in implementing PROs in research information systems. The purpose of this case study is to describe a novel information system for electronic PROs and lessons learned in implementing that system to support research in an academic health center. The system incorporates freely available and commercial software and involves clinical and research workflows that support the collection, transformation, and research use of PRO data. The software and processes that comprise the system serve three main functions, (i) collecting electronic PROs in clinical care, (ii) integrating PRO data with non-patient generated clinical data, and (iii) disseminating data to researchers through the institution's research informatics infrastructure, including the i2b2 (Informatics for Integrating Biology and the Bedside) system. Our successful design and implementation was driven by three overarching strategies. First, we selected and implemented multiple interfaced technologies to support PRO collection, management, and research use. Second, we aimed to use standardized approaches to measuring PROs, sending PROs between systems, and disseminating PROs. Finally, we focused on using technologies and processes that aligned with existing clinical research information management strategies within our organization. These experiences and lessons may help future implementers and researchers enhance the scale and sustainable use of systems for research use of PROs.

A strategy to establish Food Safety Model Repositories.

PubMed

Plaza-Rodríguez, C; Thoens, C; Falenski, A; Weiser, A A; Appel, B; Kaesbohrer, A; Filter, M

2015-07-02

Transferring the knowledge of predictive microbiology into real world food manufacturing applications is still a major challenge for the whole food safety modelling community. To facilitate this process, a strategy for creating open, community driven and web-based predictive microbial model repositories is proposed. These collaborative model resources could significantly improve the transfer of knowledge from research into commercial and governmental applications and also increase efficiency, transparency and usability of predictive models. To demonstrate the feasibility, predictive models of Salmonella in beef previously published in the scientific literature were re-implemented using an open source software tool called PMM-Lab. The models were made publicly available in a Food Safety Model Repository within the OpenML for Predictive Modelling in Food community project. Three different approaches were used to create new models in the model repositories: (1) all information relevant for model re-implementation is available in a scientific publication, (2) model parameters can be imported from tabular parameter collections and (3) models have to be generated from experimental data or primary model parameters. All three approaches were demonstrated in the paper. The sample Food Safety Model Repository is available via: http://sourceforge.net/projects/microbialmodelingexchange/files/models and the PMM-Lab software can be downloaded from http://sourceforge.net/projects/pmmlab/. This work also illustrates that a standardized information exchange format for predictive microbial models, as the key component of this strategy, could be established by adoption of resources from the Systems Biology domain. Copyright © 2015. Published by Elsevier B.V.

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

ERIC Educational Resources Information Center

Hasenekoglu, Ismet; Timucin, Melih

2007-01-01

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

Implementing Genome-Driven Oncology

PubMed Central

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

2017-01-01

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

Public Understanding of Plant Biology: Voices from the Bottom of the Garden

ERIC Educational Resources Information Center

Watts, Mike

2015-01-01

Many household gardeners accumulate considerable knowledge of plant biology through a range of informal learning sources. This knowledge seldom relates to school biology and is driven by interest, keen motivation and what is termed here "vital relevance." A small opportunity sample of 12 gardeners (6 M, 6 F) is interviewed in terms of…

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

PubMed

Pal, Parimal; Thakura, Ritwik; Chakrabortty, Sankha

2016-05-01

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

Intra- and interrater reliability of the Chicago Classification of achalasia subtypes in pediatric high-resolution esophageal manometry (HRM) recordings.

PubMed

Singendonk, M M J; Rosen, R; Oors, J; Rommel, N; van Wijk, M P; Benninga, M A; Nurko, S; Omari, T I

2017-11-01

Subtyping achalasia by high-resolution manometry (HRM) is clinically relevant as response to therapy and prognosis have shown to vary accordingly. The aim of this study was to assess inter- and intrarater reliability of diagnosing achalasia and achalasia subtyping in children using the Chicago Classification (CC) V3.0. Six observers analyzed 40 pediatric HRM recordings (22 achalasia and 18 non-achalasia) twice by using dedicated analysis software (ManoView 3.0, Given Imaging, Los Angeles, CA, USA). Integrated relaxation pressure (IRP4s), distal contractile integral (DCI), intrabolus pressurization pattern (IBP), and distal latency (DL) were extracted and analyzed hierarchically. Cohen's κ (2 raters) and Fleiss' κ (>2 raters) and the intraclass correlation coefficient (ICC) were used for categorical and ordinal data, respectively. Based on the results of dedicated analysis software only, intra- and interrater reliability was excellent and moderate (κ=0.89 and κ=0.52, respectively) for differentiating achalasia from non-achalasia. For subtyping achalasia, reliability decreased to substantial and fair (κ=0.72 and κ=0.28, respectively). When observers were allowed to change the software-driven diagnosis according to their own interpretation of the manometric patterns, intra- and interrater reliability increased for diagnosing achalasia (κ=0.98 and κ=0.92, respectively) and for subtyping achalasia (κ=0.79 and κ=0.58, respectively). Intra- and interrater agreement for diagnosing achalasia when using HRM and the CC was very good to excellent when results of automated analysis software were interpreted by experienced observers. More variability was seen when relying solely on the software-driven diagnosis and for subtyping achalasia. Therefore, diagnosing and subtyping achalasia should be performed in pediatric motility centers with significant expertise. © 2017 John Wiley & Sons Ltd.

Flight code validation simulator

NASA Astrophysics Data System (ADS)

Sims, Brent A.

1996-05-01

An End-To-End Simulation capability for software development and validation of missile flight software on the actual embedded computer has been developed utilizing a 486 PC, i860 DSP coprocessor, embedded flight computer and custom dual port memory interface hardware. This system allows real-time interrupt driven embedded flight software development and checkout. The flight software runs in a Sandia Digital Airborne Computer and reads and writes actual hardware sensor locations in which Inertial Measurement Unit data resides. The simulator provides six degree of freedom real-time dynamic simulation, accurate real-time discrete sensor data and acts on commands and discretes from the flight computer. This system was utilized in the development and validation of the successful premier flight of the Digital Miniature Attitude Reference System in January of 1995 at the White Sands Missile Range on a two stage attitude controlled sounding rocket.

Biological control of aragonite formation in stony corals

NASA Astrophysics Data System (ADS)

Von Euw, Stanislas; Zhang, Qihong; Manichev, Viacheslav; Murali, Nagarajan; Gross, Juliane; Feldman, Leonard C.; Gustafsson, Torgny; Flach, Carol; Mendelsohn, Richard; Falkowski, Paul G.

2017-06-01

Little is known about how stony corals build their calcareous skeletons. There are two prevailing hypotheses: that it is a physicochemically dominated process and that it is a biologically mediated one. Using a combination of ultrahigh-resolution three-dimensional imaging and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy, we show that mineral deposition is biologically driven. Randomly arranged, amorphous nanoparticles are initially deposited in microenvironments enriched in organic material; they then aggregate and form ordered aragonitic structures through crystal growth by particle attachment. Our NMR results are consistent with heterogeneous nucleation of the solid mineral phase driven by coral acid-rich proteins. Such a mechanism suggests that stony corals may be able to sustain calcification even under lower pH conditions that do not favor the inorganic precipitation of aragonite.

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

VirtualPlant: A Software Platform to Support Systems Biology Research1[W][OA

PubMed Central

Katari, Manpreet S.; Nowicki, Steve D.; Aceituno, Felipe F.; Nero, Damion; Kelfer, Jonathan; Thompson, Lee Parnell; Cabello, Juan M.; Davidson, Rebecca S.; Goldberg, Arthur P.; Shasha, Dennis E.; Coruzzi, Gloria M.; Gutiérrez, Rodrigo A.

2010-01-01

Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data, its data structures, algorithms, and visualization tools are designed in a species-independent way. VirtualPlant is freely available at www.virtualplant.org. PMID:20007449

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

PubMed

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

2013-03-01

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

From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform.

PubMed

Weckwerth, Wolfram; Wienkoop, Stefanie; Hoehenwarter, Wolfgang; Egelhofer, Volker; Sun, Xiaoliang

2014-01-01

Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a fundamental technique of this novel research area as it is the basis for gene function analysis and modeling of dynamic protein networks. Here a complete proteomics platform suited for functional genomics and systems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment; http://www.univie.ac.at/mosys/software.html ) as a rapid exploratory analysis step; MASS WESTERN for targeted proteomics; COVAIN ( http://www.univie.ac.at/mosys/software.html ) for multivariate statistical analysis, data integration, and data mining; and PROMEX ( http://www.univie.ac.at/mosys/databases.html ) as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affinity chromatography) with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data using this platform are presented. All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html.

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.

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.

Deglacial diatom production in the tropical North Atlantic driven by enhanced silicic acid supply

NASA Astrophysics Data System (ADS)

Hendry, Katharine R.; Gong, Xun; Knorr, Gregor; Pike, Jennifer; Hall, Ian R.

2016-03-01

Major shifts in ocean circulation are thought to be responsible for abrupt changes in temperature and atmospheric CO2 during the last deglaciation, linked to variability in meridional heat transport and deep ocean carbon storage. There is also widespread evidence for shifts in biological production during these times of deglacial CO2 rise, including enhanced diatom production in regions such as the tropical Atlantic. However, it remains unclear as to whether this diatom production was driven by enhanced wind-driven upwelling or density-driven vertical mixing, or by elevated thermocline concentrations of silicic acid supplied to the surface at a constant rate. Here, we demonstrate that silicic acid supply at depth in the NE Atlantic was enhanced during the abrupt climate events of the deglaciation. We use marine sediment archives to show that an increase in diatom production during abrupt climate shifts could only occur in regions of the NE Atlantic where the deep supply of silicic acid could reach the surface. The associated changes are indicative of enhanced regional wind-driven upwelling and/or weakened stratification due to circulation changes during phases of weakened Atlantic meridional overturning. Globally near-synchronous pulses of diatom production and enhanced thermocline concentrations of silicic acid suggest that widespread deglacial surface-driven breakdown of stratification, linked to changes in atmospheric circulation, had major consequences for biological productivity and carbon cycling.

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares

PubMed Central

Bonnet, Agnès; Lagarrigue, Sandrine; Liaubet, Laurence; Robert-Granié, Christèle; SanCristobal, Magali; Tosser-Klopp, Gwenola

2009-01-01

Background As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results. Results GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation. Conclusion Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated). PMID:19615111

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

PubMed

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

2017-09-01

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

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

NASA Technical Reports Server (NTRS)

Dehghani, Navid; Tankenson, Michael

2006-01-01

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

Electrophoretic interactions and aggregation of colloidal biological particles

NASA Technical Reports Server (NTRS)

Davis, Robert H.; Nichols, Scott C.; Loewenberg, Michael; Todd, Paul

1994-01-01

The separation of cells or particles from solution has traditionally been accomplished with centrifuges or by sedimentation; however, many particles have specific densities close to unity, making buoyancy-driven motion slow or negligible, but most cells and particles carry surface charges, making them ideal for electrophoretic separation. Both buoyancy-driven and electrophoretic separation may be influenced by hydrodynamic interactions and aggregation of neighboring particles. Aggregation by electrophoresis was analyzed for two non-Brownian particles with different zeta potentials and thin double layers migrating through a viscous fluid. The results indicate that the initial rate of electrophoretically-driven aggregation may exceed that of buoyancy-driven aggregation, even under conditions in which buoyancy-driven relative motion of noninteracting particles is dominant.

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.

Utilising database-driven interactive software to enhance independent home-study in a flipped classroom setting: going beyond visualising engineering concepts to ensuring formative assessment

NASA Astrophysics Data System (ADS)

Comerford, Liam; Mannis, Adam; DeAngelis, Marco; Kougioumtzoglou, Ioannis A.; Beer, Michael

2018-07-01

The concept of formative assessment is considered by many to play an important role in enhancing teaching in higher engineering education. In this paper, the concept of the flipped classroom as part of a blended learning curriculum is highlighted as an ideal medium through which formative assessment practices arise. Whilst the advantages of greater interaction between students and lecturers in classes are numerous, there are often clear disadvantages associated with the independent home-study component that complements timetabled sessions in a flipped classroom setting, specifically, the popular method of replacing traditional classroom teaching with video lectures. This leads to a clear lack of assurances that the cited benefits of a flipped classroom approach are echoed in the home-study arena. Over the past three years, the authors have sought to address identified deficiencies in this area of blended learning through the development of database-driven e-learning software with the capability of introducing formative assessment practices to independent home-study. This paper maps out aspects of two specific evolving practices at separate institutions, from which guiding principles of incorporating formative assessment aspects into e-learning software are identified and highlighted in the context of independent home-study as part of a flipped classroom approach.

GenePRIMP: A software quality control tool

ScienceCinema

Amrita Pati

2017-12-09

Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

15 CFR 740.7 - Computers (APP).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 4A003. (2) Technology and software. License Exception APP authorizes exports of technology and software... programmability. (ii) Technology and source code. Technology and source code eligible for License Exception APP..., reexports and transfers (in-country) for nuclear, chemical, biological, or missile end-users and end-uses...

SNPversity: A web-based tool for visualizing diversity

USDA-ARS?s Scientific Manuscript database

Background: Many stand-alone desktop software suites exist to visualize single nucleotide polymorphisms (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualizat...

Virtual immunology: software for teaching basic immunology.

PubMed

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

2013-01-01

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

Disciplinary reporting affects the interpretation of climate change impacts in global oceans.

PubMed

Hauser, Donna D W; Tobin, Elizabeth D; Feifel, Kirsten M; Shah, Vega; Pietri, Diana M

2016-01-01

Climate change is affecting marine ecosystems, but different investigative approaches in physical, chemical, and biological disciplines may influence interpretations of climate-driven changes in the ocean. Here, we review the ocean change literature from 2007 to 2012 based on 461 of the most highly cited studies in physical and chemical oceanography and three biological subdisciplines. Using highly cited studies, we focus on research that has shaped recent discourse on climate-driven ocean change. Our review identified significant differences in spatial and temporal scales of investigation among disciplines. Physical/chemical studies had a median duration of 29 years (n = 150) and covered the greatest study areas (median 1.41 × 10(7) km(2) , n = 148). Few biological studies were conducted over similar spatial and temporal scales (median 8 years, n = 215; median 302 km(2) , n = 196), suggesting a more limited ability to separate climate-related responses from natural variability. We linked physical/chemical and biological disciplines by tracking studies examining biological responses to changing ocean conditions. Of the 545 biological responses recorded, a single physical or chemical stressor was usually implicated as the cause (59%), with temperature as the most common primary stressor (44%). The most frequently studied biological responses were changes in physiology (31%) and population abundance (30%). Differences in disciplinary studies, as identified in this review, can ultimately influence how researchers interpret climate-related impacts in marine systems. We identified research gaps and the need for more discourse in (1) the Indian and other Southern Hemisphere ocean basins; (2) research themes such as archaea, bacteria, viruses, mangroves, turtles, and ocean acidification; (3) physical and chemical stressors such as dissolved oxygen, salinity, and upwelling; and (4) adaptive responses of marine organisms to climate-driven ocean change. Our findings reveal that highly cited biological studies are rarely conducted on scales that match those of physical and chemical studies. Rather, we suggest a need for measuring responses at biologically relevant scales. © 2015 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Outcomes of a Research-Driven Laboratory and Literature Course Designed to Enhance Undergraduate Contributions to Original Research

ERIC Educational Resources Information Center

Rasche, Madeline E.

2004-01-01

This work describes outcomes of a research-driven advanced microbiology laboratory and literature research course intended to enhance undergraduate preparation for and contributions to original research. The laboratory section was designed to teach fundamental biochemistry and molecular biology techniques in the context of an original research…

Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological?

PubMed

Richards, Emilie J; Brown, Jeremy M; Barley, Anthony J; Chong, Rebecca A; Thomson, Robert C

2018-02-19

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

Software Tools for Emittance Measurement and Matching for 12 GeV CEBAF

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

Turner, Dennis L.

2016-05-01

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

Software for System for Controlling a Magnetically Levitated Rotor

NASA Technical Reports Server (NTRS)

Morrison, Carlos R. (Inventor)

2004-01-01

In a rotor assembly having a rotor supported for rotation by magnetic bearings, a processor controlled by software or firmware controls the generation of force vectors that position the rotor relative to its bearings in a 'bounce' mode in which the rotor axis is displaced from the principal axis defined between the bearings and a 'tilt' mode in which the rotor axis is tilted or inclined relative to the principal axis. Waveform driven perturbations are introduced to generate force vectors that excite the rotor in either the 'bounce' or 'tilt' modes.

A synchronized computational architecture for generalized bilateral control of robot arms

NASA Technical Reports Server (NTRS)

Bejczy, Antal K.; Szakaly, Zoltan

1987-01-01

This paper describes a computational architecture for an interconnected high speed distributed computing system for generalized bilateral control of robot arms. The key method of the architecture is the use of fully synchronized, interrupt driven software. Since an objective of the development is to utilize the processing resources efficiently, the synchronization is done in the hardware level to reduce system software overhead. The architecture also achieves a balaced load on the communication channel. The paper also describes some architectural relations to trading or sharing manual and automatic control.

Extraordinary Oscillations of an Ordinary Forced Pendulum

ERIC Educational Resources Information Center

Butikov, Eugene I.

2008-01-01

Several well-known and newly discovered counterintuitive regular and chaotic modes of the sinusoidally driven rigid planar pendulum are discussed and illustrated by computer simulations. The software supporting the investigation offers many interesting predefined examples that demonstrate various peculiarities of this famous physical model.…

2005 5th Annual CMMI Technology Conference and User Group. Volume 4: Thursday

DTIC Science & Technology

2005-11-17

Identification and Involvement in the CMMI, Mr. James R. Armstrong , Systems and Software Consortium Ensuring the Right Process is Deployed Right...Customer-Driven Organization Chart Marketing Management: Analysis, Planning, Implementation and Control Philip Kotler © Prentice Hall Being Customer

Pile/shaft designs using artificial neural networks (i.e., genetic programming) with spatial variability considerations : [summary].

DOT National Transportation Integrated Search

2014-03-01

In this project, University of Florida researchers : sought to improve the unit skin friction and tip : resistance correlations embedded in the FB-Deep : software algorithm for estimating driven pile and : drilled shaft resistance. They utilized an a...

Computer Microtechnology for a Severely Disabled Preschool Child.

ERIC Educational Resources Information Center

Douglas, J.; And Others

1988-01-01

The case study describes microtechnological aids for a quadriplegic preschool aged boy dependent on a ventilator via a tracheostomy. Provision of a computer, a variety of specially designed switches and software, together with a self-driven powered wheelchair maximized expression of his developmental needs. (DB)

Metadata-driven Clinical Data Loading into i2b2 for Clinical and Translational Science Institutes.

PubMed

Post, Andrew R; Pai, Akshatha K; Willard, Richard; May, Bradley J; West, Andrew C; Agravat, Sanjay; Granite, Stephen J; Winslow, Raimond L; Stephens, David S

2016-01-01

Clinical and Translational Science Award (CTSA) recipients have a need to create research data marts from their clinical data warehouses, through research data networks and the use of i2b2 and SHRINE technologies. These data marts may have different data requirements and representations, thus necessitating separate extract, transform and load (ETL) processes for populating each mart. Maintaining duplicative procedural logic for each ETL process is onerous. We have created an entirely metadata-driven ETL process that can be customized for different data marts through separate configurations, each stored in an extension of i2b2 's ontology database schema. We extended our previously reported and open source Eureka! Clinical Analytics software with this capability. The same software has created i2b2 data marts for several projects, the largest being the nascent Accrual for Clinical Trials (ACT) network, for which it has loaded over 147 million facts about 1.2 million patients.

Metadata-driven Clinical Data Loading into i2b2 for Clinical and Translational Science Institutes

PubMed Central

Post, Andrew R.; Pai, Akshatha K.; Willard, Richard; May, Bradley J.; West, Andrew C.; Agravat, Sanjay; Granite, Stephen J.; Winslow, Raimond L.; Stephens, David S.

2016-01-01

Clinical and Translational Science Award (CTSA) recipients have a need to create research data marts from their clinical data warehouses, through research data networks and the use of i2b2 and SHRINE technologies. These data marts may have different data requirements and representations, thus necessitating separate extract, transform and load (ETL) processes for populating each mart. Maintaining duplicative procedural logic for each ETL process is onerous. We have created an entirely metadata-driven ETL process that can be customized for different data marts through separate configurations, each stored in an extension of i2b2 ‘s ontology database schema. We extended our previously reported and open source Eureka! Clinical Analytics software with this capability. The same software has created i2b2 data marts for several projects, the largest being the nascent Accrual for Clinical Trials (ACT) network, for which it has loaded over 147 million facts about 1.2 million patients. PMID:27570667

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

NASA Astrophysics Data System (ADS)

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

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

Adopting best practices: "Agility" moves from software development to healthcare project management.

PubMed

Kitzmiller, Rebecca; Hunt, Eleanor; Sproat, Sara Breckenridge

2006-01-01

It is time for a change in mindset in how nurses operationalize system implementations and manage projects. Computers and systems have evolved over time from unwieldy mysterious machines of the past to ubiquitous computer use in every aspect of daily lives and work sites. Yet, disconcertingly, the process used to implement these systems has not evolved. Technology implementation does not need to be a struggle. It is time to adapt traditional plan-driven implementation methods to incorporate agile techniques. Agility is a concept borrowed from software development and is presented here because it encourages flexibility, adaptation, and continuous learning as part of the implementation process. Agility values communication and harnesses change to an advantage, which facilitates the natural evolution of an adaptable implementation process. Specific examples of agility in an implementation are described, and plan-driven implementation stages are adapted to incorporate relevant agile techniques. This comparison demonstrates how an agile approach enhances traditional implementation techniques to meet the demands of today's complex healthcare environments.

Table-driven configuration and formatting of telemetry data in the Deep Space Network

NASA Technical Reports Server (NTRS)

Manning, Evan

1994-01-01

With a restructured software architecture for telemetry system control and data processing, the NASA/Deep Space Network (DSN) has substantially improved its ability to accommodate a wide variety of spacecraft in an era of 'better, faster, cheaper'. In the new architecture, the permanent software implements all capabilities needed by any system user, and text tables specify how these capabilities are to be used for each spacecraft. Most changes can now be made rapidly, outside of the traditional software development cycle. The system can be updated to support a new spacecraft through table changes rather than software changes, reducing the implementation, test, and delivery cycle for such a change from three months to three weeks. The mechanical separation of the text table files from the program software, with tables only loaded into memory when that mission is being supported, dramatically reduces the level of regression testing required. The format of each table is a different compromise between ease of human interpretation, efficiency of computer interpretation, and flexibility.

Integrating systems biology models and biomedical ontologies

PubMed Central

2011-01-01

Background Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. Results We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. Conclusions We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms. PMID:21835028

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

PubMed

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

2016-02-03

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

A software communication tool for the tele-ICU.

PubMed

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

2013-01-01

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

Caught in Their Tracks

ERIC Educational Resources Information Center

Pacifici, Lara

2008-01-01

By allowing students to develop and conduct research on biological or environmental problems they identify themselves, students gain a higher level of understanding and appreciation for science. To this end, teachers should incorporate student-driven research in biology and environmental science classes in lieu of cookbook laboratory activities…

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

PubMed

Swertz, Morris A; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K; Kanterakis, Alexandros; Roos, Erik T; Lops, Joris; Thorisson, Gudmundur A; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J; de Brock, Engbert O; Jansen, Ritsert C; Parkinson, Helen

2010-12-21

There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

The use of writing assignments to help students synthesize content in upper-level undergraduate biology courses.

PubMed

Sparks-Thissen, Rebecca L

2017-02-01

Biology education is undergoing a transformation toward a more student-centered, inquiry-driven classroom. Many educators have designed engaging assignments that are designed to help undergraduate students gain exposure to the scientific process and data analysis. One of these types of assignments is use of a grant proposal assignment. Many instructors have used these assignments in lecture-based courses to help students process information in the literature and apply that information to a novel problem such as design of an antiviral drug or a vaccine. These assignments have been helpful in engaging students in the scientific process in the absence of an inquiry-driven laboratory. This commentary discusses the application of these grant proposal writing assignments to undergraduate biology courses. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biological control of aragonite formation in stony corals.

PubMed

Von Euw, Stanislas; Zhang, Qihong; Manichev, Viacheslav; Murali, Nagarajan; Gross, Juliane; Feldman, Leonard C; Gustafsson, Torgny; Flach, Carol; Mendelsohn, Richard; Falkowski, Paul G

2017-06-02

Little is known about how stony corals build their calcareous skeletons. There are two prevailing hypotheses: that it is a physicochemically dominated process and that it is a biologically mediated one. Using a combination of ultrahigh-resolution three - dimensional imaging and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy, we show that mineral deposition is biologically driven. Randomly arranged, amorphous nanoparticles are initially deposited in microenvironments enriched in organic material; they then aggregate and form ordered aragonitic structures through crystal growth by particle attachment. Our NMR results are consistent with heterogeneous nucleation of the solid mineral phase driven by coral acid-rich proteins. Such a mechanism suggests that stony corals may be able to sustain calcification even under lower pH conditions that do not favor the inorganic precipitation of aragonite. Copyright © 2017, American Association for the Advancement of Science.

Model-Driven Useware Engineering

NASA Astrophysics Data System (ADS)

Meixner, Gerrit; Seissler, Marc; Breiner, Kai

User-oriented hardware and software development relies on a systematic development process based on a comprehensive analysis focusing on the users' requirements and preferences. Such a development process calls for the integration of numerous disciplines, from psychology and ergonomics to computer sciences and mechanical engineering. Hence, a correspondingly interdisciplinary team must be equipped with suitable software tools to allow it to handle the complexity of a multimodal and multi-device user interface development approach. An abstract, model-based development approach seems to be adequate for handling this complexity. This approach comprises different levels of abstraction requiring adequate tool support. Thus, in this chapter, we present the current state of our model-based software tool chain. We introduce the use model as the core model of our model-based process, transformation processes, and a model-based architecture, and we present different software tools that provide support for creating and maintaining the models or performing the necessary model transformations.

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

NASA Astrophysics Data System (ADS)

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

2008-07-01

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

Space station dynamics, attitude control and momentum management

NASA Technical Reports Server (NTRS)

Sunkel, John W.; Singh, Ramen P.; Vengopal, Ravi

1989-01-01

The Space Station Attitude Control System software test-bed provides a rigorous environment for the design, development and functional verification of GN and C algorithms and software. The approach taken for the simulation of the vehicle dynamics and environmental models using a computationally efficient algorithm is discussed. The simulation includes capabilities for docking/berthing dynamics, prescribed motion dynamics associated with the Mobile Remote Manipulator System (MRMS) and microgravity disturbances. The vehicle dynamics module interfaces with the test-bed through the central Communicator facility which is in turn driven by the Station Control Simulator (SCS) Executive. The Communicator addresses issues such as the interface between the discrete flight software and the continuous vehicle dynamics, and multi-programming aspects such as the complex flow of control in real-time programs. Combined with the flight software and redundancy management modules, the facility provides a flexible, user-oriented simulation platform.

From Exotic to Mainstream: A 10-year Odyssey from Internet Speed to Boundary Spanning with Scrum

NASA Astrophysics Data System (ADS)

Baskerville, Richard; Pries-Heje, Jan; Madsen, Sabine

Based on four empirical studies conducted over a 10-year time period from 1999 to 2008 we investigate how local software processes interact with global changes in the software development context. In 1999 companies were developing software at high speed in a desperate rush to be first-to-market. In 2001 a new high speed/quick results development process had become established practice. In 2003 changes in the market created the need for a more balanced view on speed and quality, and in 2008 companies were successfully combining agile and plan driven approaches to achieve the benefits of both. The studies reveal a twostage pattern in which dramatic changes in the market causes disruption of established practices, experimentation, and process adaptations followed by consolidation of lessons learnt into a new (and once again mature) software development process. Limitations, implications, and areas for future research are discussed.

Professional Ethics of Software Engineers: An Ethical Framework.

PubMed

Lurie, Yotam; Mark, Shlomo

2016-04-01

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

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

PubMed

Sanderson, Lacey-Anne; Ficklin, Stephen P; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A; Bett, Kirstin E; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

PubMed Central

Sanderson, Lacey-Anne; Ficklin, Stephen P.; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A.; Bett, Kirstin E.; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including ‘Feature Map’, ‘Genetic’, ‘Publication’, ‘Project’, ‘Contact’ and the ‘Natural Diversity’ modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. Database URL: http://tripal.info/ PMID:24163125

Agent-Based Phytoplankton Models of Cellular and Population Processes: Fostering Individual-Based Learning in Undergraduate Research

NASA Astrophysics Data System (ADS)

Berges, J. A.; Raphael, T.; Rafa Todd, C. S.; Bate, T. C.; Hellweger, F. L.

2016-02-01

Engaging undergraduate students in research projects that require expertise in multiple disciplines (e.g. cell biology, population ecology, and mathematical modeling) can be challenging because they have often not developed the expertise that allows them to participate at a satisfying level. Use of agent-based modeling can allow exploration of concepts at more intuitive levels, and encourage experimentation that emphasizes processes over computational skills. Over the past several years, we have involved undergraduate students in projects examining both ecological and cell biological aspects of aquatic microbial biology, using the freely-downloadable, agent-based modeling environment NetLogo (https://ccl.northwestern.edu/netlogo/). In Netlogo, actions of large numbers of individuals can be simulated, leading to complex systems with emergent behavior. The interface features appealing graphics, monitors, and control structures. In one example, a group of sophomores in a BioMathematics program developed an agent-based model of phytoplankton population dynamics in a pond ecosystem, motivated by observed macroscopic changes in cell numbers (due to growth and death), and driven by responses to irradiance, temperature and a limiting nutrient. In a second example, junior and senior undergraduates conducting Independent Studies created a model of the intracellular processes governing stress and cell death for individual phytoplankton cells (based on parameters derived from experiments using single-cell culturing and flow cytometry), and then this model was embedded in the agents in the pond ecosystem model. In our experience, students with a range of mathematical abilities learned to code quickly and could use the software with varying degrees of sophistication, for example, creation of spatially-explicit two and three-dimensional models. Skills developed quickly and transferred readily to other platforms (e.g. Matlab).

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

PubMed

Duck, Geraint; Nenadic, Goran; Filannino, Michele; Brass, Andy; Robertson, David L; Stevens, Robert

2016-01-01

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

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

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

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

The Utility of Handheld Programmable Calculators in Aircraft Life Cycle Cost Estimation.

DTIC Science & Technology

1982-09-01

are available for extended mem - ory, hardcopy printout, video interface, and special application software. Any calculator of comparable memory could...condi- tioning system. OG Total number of engine, air turbine motor (ATM) and auxiliary power unit (APU) driven generator/alternators. OHP Total number

Integration of the NRL Digital Library.

ERIC Educational Resources Information Center

King, James

2001-01-01

The Naval Research Laboratory (NRL) Library has identified six primary areas that need improvement: infrastructure, InfoWeb, TORPEDO Ultra, journal data management, classified data, and linking software. It is rebuilding InfoWeb and TORPEDO Ultra as database-driven Web applications, upgrading the STILAS library catalog, and creating other support…

Testing Evolutionary Hypotheses in the Classroom with MacClade Software.

ERIC Educational Resources Information Center

Codella, Sylvio G.

2002-01-01

Introduces MacClade which is a Macintosh-based software package that uses the techniques of cladistic analysis to explore evolutionary patterns. Describes a novel and effective exercise that allows undergraduate biology majors to test a hypothesis about behavioral evolution in insects. (Contains 13 references.) (Author/YDS)

PHARMAVIRTUA: Educational Software for Teaching and Learning Basic Pharmacology

ERIC Educational Resources Information Center

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

2014-01-01

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

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

Vogt, J R

A total of 75 papers were presented on nuclear methods for analysis of environmental and biological samples. Sessions were devoted to software and mathematical methods; nuclear methods in atmospheric and water research; nuclear and atomic methodology; nuclear methods in biology and medicine; and nuclear methods in energy research.

Future Technology-Driven Revolutions in Military Operations. Results of a Workshop

DTIC Science & Technology

1994-01-01

sensor missions. "• Biomolecular Electronics - The use of techniques from molecular biology and biotechnology to develop new molecular electronic materials...34* Biomolecular electronics - The use of techniques from molecular biology and biotechnology to develop new molecular electronic materials, components, and...occurring in molecular biology . 42 Biotechnology Molecular Biologists Arm Develoni "Magical" Caoabilitles "• To mynthsieh genm (frm satch) with conboi

EVALUATION OF TOXICITY BY OIL FLY-ASHES IN RAT ALVEOLAR EPITHELIAL CELLS: ROLE OF FENTON DRIVEN OH-RADICAL GENERATION AND PARATICLE FRACTION

EPA Science Inventory

Leachable transition metals are considered to be important mediators in the biological effects of ambient particulate matter (PM) and model particles such as oil-fly ashes (OFA). We determined metal driven Fenton activity in 10 OFA in the presence of hydrogen peroxide using elect...

A variable-instar climate-driven individual beetle-based phenology model for the invasive Asian longhorned beetle (Coleoptera: Cerambycidae)

Treesearch

R. Talbot Trotter, III; Melody A. Keena

2016-01-01

Efforts to manage and eradicate invasive species can benefit from an improved understanding of the physiology, biology, and behavior of the target species, and ongoing efforts to eradicate the Asian longhorned beetle (Anoplophora glabripennis Motschulsky) highlight the roles this information may play. Here, we present a climate-driven phenology...

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

PubMed

Wear, L L

1994-02-01

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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Bioinformatics.

PubMed

Moore, Jason H

2007-11-01

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.

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

NASA Astrophysics Data System (ADS)

Miles, B.; Band, L. E.

2013-12-01

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

USER'S GUIDE FOR GLOED VERSION 1.0 - THE GLOBAL EMISSIONS DATABASE

EPA Science Inventory

The document is a user's guide for the EPA-developed, powerful software package, Global Emissions Database (GloED). GloED is a user-friendly, menu-driven tool for storing and retrieving emissions factors and activity data on a country-specific basis. Data can be selected from dat...

PechaKucha Presentations: Teaching Storytelling, Visual Design, and Conciseness

ERIC Educational Resources Information Center

Lucas, Kristen; Rawlins, Jacob D.

2015-01-01

When speakers rely too heavily on presentation software templates, they often end up stultifying audiences with a triple-whammy of bullet points. In this article, Lucas and Rawlins present an alternative method--PechaKucha (the Japanese word for "chit chat")--a presentation style driven by a carefully planned, automatically timed…

Status of Ongoing Work in Software TRAs/TRLs

DTIC Science & Technology

2010-04-29

to changes/updates being driven by corporate market dynamics • Changes not under control or under the influence of the PMO! • On programs with long...observed and reported esearc articles, peer- reviewed white papers, point papers, early conceptual models n a ca em c , experimental as c researc

Online Patent Searching: Guided by an Expert System.

ERIC Educational Resources Information Center

Ardis, Susan B.

1990-01-01

Describes the development of an expert system for online patent searching that uses menu driven software to interpret the user's knowledge level and the general nature of the search problem. The discussion covers the rationale for developing such a system, current system functions, cost effectiveness, user reactions, and plans for future…

A Model-Driven Approach to Teaching Concurrency

ERIC Educational Resources Information Center

Carro, Manuel; Herranz, Angel; Marino, Julio

2013-01-01

We present an undergraduate course on concurrent programming where formal models are used in different stages of the learning process. The main practical difference with other approaches lies in the fact that the ability to develop correct concurrent software relies on a systematic transformation of formal models of inter-process interaction (so…

Moving Past "Hello World": Learning to Mod in an Online Affinity Space

ERIC Educational Resources Information Center

Subramanian, Shree Durga

2012-01-01

Game modding has increasingly become a mainstream and "cutting edge" medium to foster a broad range of critical software design and programming practices to learners coming from wide-ranging educational and professional backgrounds. Participatory practices, like game modding, are highly interest-driven and entail intense engagement with…

An Implemented Strategy for Campus Connectivity and Cooperative Computing.

ERIC Educational Resources Information Center

Halaris, Antony S.; Sloan, Lynda W.

1989-01-01

ConnectPac, a software package developed at Iona College to allow a computer user to access all services from a single personal computer, is described. ConnectPac uses mainframe computing to support a campus computing network, integrating personal and centralized computing into a menu-driven user environment. (Author/MLW)

Multimedia Madness: Creating with a Purpose

ERIC Educational Resources Information Center

Bodley, Barb; Bremer, Janet

2004-01-01

High school students working in a project-driven environment create "projects with a purpose" that give younger students technology-based activities to help them practice skills in reading, math, spelling and science. An elective semester-long course using the Macromedia suite of programs with the objective of learning the software skills of…

Ontology-Driven Discovery of Scientific Computational Entities

ERIC Educational Resources Information Center

Brazier, Pearl W.

2010-01-01

Many geoscientists use modern computational resources, such as software applications, Web services, scientific workflows and datasets that are readily available on the Internet, to support their research and many common tasks. These resources are often shared via human contact and sometimes stored in data portals; however, they are not necessarily…

Internet Database Review: The FDA BBS.

ERIC Educational Resources Information Center

Tomaiuolo, Nicholas G.

1993-01-01

Describes the electronic bulletin board system (BBS) of the Food and Drug Administration (FDA) that is accessible through the Internet. Highlights include how to gain access; the menu-driven software; other electronic sources of FDA information; and adding value. Examples of the FDA BBS menu and the help screen are included. (LRW)

Climate Change Effects on Stream and River Biological Indicators: A Preliminary Analysis (External Review Draft)

EPA Science Inventory

This draft report is a preliminary assessment that describes how biological indicators are likely to respond to climate change, how well current sampling schemes may detect climate-driven changes, and how likely it is that these sampling schemes will continue to detect impairment...

Database Driven 6-DOF Trajectory Simulation for Debris Transport Analysis

NASA Technical Reports Server (NTRS)

West, Jeff

2008-01-01

Debris mitigation and risk assessment have been carried out by NASA and its contractors supporting Space Shuttle Return-To-Flight (RTF). As a part of this assessment, analysis of transport potential for debris that may be liberated from the vehicle or from pad facilities prior to tower clear (Lift-Off Debris) is being performed by MSFC. This class of debris includes plume driven and wind driven sources for which lift as well as drag are critical for the determination of the debris trajectory. As a result, NASA MSFC has a need for a debris transport or trajectory simulation that supports the computation of lift effect in addition to drag without the computational expense of fully coupled CFD with 6-DOF. A database driven 6-DOF simulation that uses aerodynamic force and moment coefficients for the debris shape that are interpolated from a database has been developed to meet this need. The design, implementation, and verification of the database driven six degree of freedom (6-DOF) simulation addition to the Lift-Off Debris Transport Analysis (LODTA) software are discussed in this paper.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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.

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

PubMed Central

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

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

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

PubMed

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

2015-04-01

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

Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards.

PubMed

Percy, Andrew J; Yang, Juncong; Chambers, Andrew G; Borchers, Christoph H

2016-01-01

Absolute quantitative strategies are emerging as a powerful and preferable means of deriving concentrations in biological samples for systems biology applications. Method development is driven by the need to establish new-and validate current-protein biomarkers of high-to-low abundance for clinical utility. In this chapter, we describe a methodology involving two-dimensional (2D) reversed-phase liquid chromatography (RPLC), operated under alkaline and acidic pH conditions, combined with multiple reaction monitoring (MRM)-mass spectrometry (MS) (also called selected reaction monitoring (SRM)-MS) and a complex mixture of stable isotope-labeled standard (SIS) peptides, to quantify a broad and diverse panel of 253 proteins in human blood plasma. The quantitation range spans 8 orders of magnitude-from 15 mg/mL (for vitamin D-binding protein) to 450 pg/mL (for protein S100-B)-and includes 31 low-abundance proteins (defined as being <10 ng/mL) of potential disease relevance. The method is designed to assess candidates at the discovery and/or verification phases of the biomarker pipeline and can be adapted to examine smaller or alternate panels of proteins for higher sample throughput. Also detailed here is the application of our recently developed software tool-Qualis-SIS-for protein quantitation (via regression analysis of standard curves) and quality assessment of the resulting data. Overall, this chapter provides the blueprint for the replication of this quantitative proteomic method by proteomic scientists of all skill levels.

Accurate evaluation and analysis of functional genomics data and methods

PubMed Central

Greene, Casey S.; Troyanskaya, Olga G.

2016-01-01

The development of technology capable of inexpensively performing large-scale measurements of biological systems has generated a wealth of data. Integrative analysis of these data holds the promise of uncovering gene function, regulation, and, in the longer run, understanding complex disease. However, their analysis has proved very challenging, as it is difficult to quickly and effectively assess the relevance and accuracy of these data for individual biological questions. Here, we identify biases that present challenges for the assessment of functional genomics data and methods. We then discuss evaluation methods that, taken together, begin to address these issues. We also argue that the funding of systematic data-driven experiments and of high-quality curation efforts will further improve evaluation metrics so that they more-accurately assess functional genomics data and methods. Such metrics will allow researchers in the field of functional genomics to continue to answer important biological questions in a data-driven manner. PMID:22268703

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

PubMed Central

Chang, Roger L; Ghamsari, Lila; Manichaikul, Ani; Hom, Erik F Y; Balaji, Santhanam; Fu, Weiqi; Shen, Yun; Hao, Tong; Palsson, Bernhard Ø; Salehi-Ashtiani, Kourosh; Papin, Jason A

2011-01-01

Metabolic network reconstruction encompasses existing knowledge about an organism's metabolism and genome annotation, providing a platform for omics data analysis and phenotype prediction. The model alga Chlamydomonas reinhardtii is employed to study diverse biological processes from photosynthesis to phototaxis. Recent heightened interest in this species results from an international movement to develop algal biofuels. Integrating biological and optical data, we reconstructed a genome-scale metabolic network for this alga and devised a novel light-modeling approach that enables quantitative growth prediction for a given light source, resolving wavelength and photon flux. We experimentally verified transcripts accounted for in the network and physiologically validated model function through simulation and generation of new experimental growth data, providing high confidence in network contents and predictive applications. The network offers insight into algal metabolism and potential for genetic engineering and efficient light source design, a pioneering resource for studying light-driven metabolism and quantitative systems biology. PMID:21811229

Water transport mechanism through open capillaries analyzed by direct surface modifications on biological surfaces

NASA Astrophysics Data System (ADS)

Ishii, Daisuke; Horiguchi, Hiroko; Hirai, Yuji; Yabu, Hiroshi; Matsuo, Yasutaka; Ijiro, Kuniharu; Tsujii, Kaoru; Shimozawa, Tateo; Hariyama, Takahiko; Shimomura, Masatsugu

2013-10-01

Some small animals only use water transport mechanisms passively driven by surface energies. However, little is known about passive water transport mechanisms because it is difficult to measure the wettability of microstructures in small areas and determine the chemistry of biological surfaces. Herein, we developed to directly analyse the structural effects of wettability of chemically modified biological surfaces by using a nanoliter volume water droplet and a hi-speed video system. The wharf roach Ligia exotica transports water only by using open capillaries in its legs containing hair- and paddle-like microstructures. The structural effects of legs chemically modified with a self-assembled monolayer were analysed, so that the wharf roach has a smart water transport system passively driven by differences of wettability between the microstructures. We anticipate that this passive water transport mechanism may inspire novel biomimetic fluid manipulations with or without a gravitational field.

A sensory-driven controller for quadruped locomotion.

PubMed

Ferreira, César; Santos, Cristina P

2017-02-01

Locomotion of quadruped robots has not yet achieved the harmony, flexibility, efficiency and robustness of its biological counterparts. Biological research showed that spinal reflexes are crucial for a successful locomotion in the most varied terrains. In this context, the development of bio-inspired controllers seems to be a good way to move toward an efficient and robust robotic locomotion, by mimicking their biological counterparts. This contribution presents a sensory-driven controller designed for the simulated Oncilla quadruped robot. In the proposed reflex controller, movement is generated through the robot's interactions with the environment, and therefore, the controller is solely dependent on sensory information. The results show that the reflex controller is capable of producing stable quadruped locomotion with a regular stepping pattern. Furthermore, it is capable of dealing with slopes without changing the parameters and with small obstacles, overcoming them successfully. Finally, system robustness was verified by adding noise to sensors and actuators and also delays.

Human factors for capacity building: lessons learned from the OpenMRS implementers network.

PubMed

Seebregts, C J; Mamlin, B W; Biondich, P G; Fraser, H S F; Wolfe, B A; Jazayeri, D; Miranda, J; Blaya, J; Sinha, C; Bailey, C T; Kanter, A S

2010-01-01

The overall objective of this project was to investigate ways to strengthen the OpenMRS community by (i) developing capacity and implementing a network focusing specifically on the needs of OpenMRS implementers, (ii) strengthening community-driven aspects of OpenMRS and providing a dedicated forum for implementation-specific issues, and; (iii) providing regional support for OpenMRS implementations as well as mentorship and training. The methods used included (i) face-to-face networking using meetings and workshops; (ii) online collaboration tools, peer support and mentorship programmes; (iii) capacity and community development programmes, and; (iv) community outreach programmes. The community-driven approach, combined with a few simple interventions, has been a key factor in the growth and success of the OpenMRS Implementers Network. It has contributed to implementations in at least twenty-three different countries using basic online tools; and provided mentorship and peer support through an annual meeting, workshops and an internship program. The OpenMRS Implementers Network has formed collaborations with several other open source networks and is evolving regional OpenMRS Centres of Excellence to provide localized support for OpenMRS development and implementation. These initiatives are increasing the range of functionality and sustainability of open source software in the health domain, resulting in improved adoption and enterprise-readiness. Social organization and capacity development activities are important in growing a successful community-driven open source software model.

Multi-Mission Power Analysis Tool (MMPAT) Version 3

NASA Technical Reports Server (NTRS)

Wood, Eric G.; Chang, George W.; Chen, Fannie C.

2012-01-01

The Multi-Mission Power Analysis Tool (MMPAT) simulates a spacecraft power subsystem including the power source (solar array and/or radioisotope thermoelectric generator), bus-voltage control, secondary battery (lithium-ion or nickel-hydrogen), thermostatic heaters, and power-consuming equipment. It handles multiple mission types including heliocentric orbiters, planetary orbiters, and surface operations. Being parametrically driven along with its user-programmable features can reduce or even eliminate any need for software modifications when configuring it for a particular spacecraft. It provides multiple levels of fidelity, thereby fulfilling the vast majority of a project s power simulation needs throughout the lifecycle. It can operate in a stand-alone mode with a graphical user interface, in batch mode, or as a library linked with other tools. This software can simulate all major aspects of a spacecraft power subsystem. It is parametrically driven to reduce or eliminate the need for a programmer. Added flexibility is provided through user-designed state models and table-driven parameters. MMPAT is designed to be used by a variety of users, such as power subsystem engineers for sizing power subsystem components; mission planners for adjusting mission scenarios using power profiles generated by the model; system engineers for performing system- level trade studies using the results of the model during the early design phases of a spacecraft; and operations personnel for high-fidelity modeling of the essential power aspect of the planning picture.

Can We Practically Bring Physics-based Modeling Into Operational Analytics Tools?

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

Granderson, Jessica; Bonvini, Marco; Piette, Mary Ann

We present that analytics software is increasingly used to improve and maintain operational efficiency in commercial buildings. Energy managers, owners, and operators are using a diversity of commercial offerings often referred to as Energy Information Systems, Fault Detection and Diagnostic (FDD) systems, or more broadly Energy Management and Information Systems, to cost-effectively enable savings on the order of ten to twenty percent. Most of these systems use data from meters and sensors, with rule-based and/or data-driven models to characterize system and building behavior. In contrast, physics-based modeling uses first-principles and engineering models (e.g., efficiency curves) to characterize system and buildingmore » behavior. Historically, these physics-based approaches have been used in the design phase of the building life cycle or in retrofit analyses. Researchers have begun exploring the benefits of integrating physics-based models with operational data analytics tools, bridging the gap between design and operations. In this paper, we detail the development and operator use of a software tool that uses hybrid data-driven and physics-based approaches to cooling plant FDD and optimization. Specifically, we describe the system architecture, models, and FDD and optimization algorithms; advantages and disadvantages with respect to purely data-driven approaches; and practical implications for scaling and replicating these techniques. Finally, we conclude with an evaluation of the future potential for such tools and future research opportunities.« less

A system for the real-time display of radar and video images of targets

NASA Technical Reports Server (NTRS)

Allen, W. W.; Burnside, W. D.

1990-01-01

Described here is a software and hardware system for the real-time display of radar and video images for use in a measurement range. The main purpose is to give the reader a clear idea of the software and hardware design and its functions. This system is designed around a Tektronix XD88-30 graphics workstation, used to display radar images superimposed on video images of the actual target. The system's purpose is to provide a platform for tha analysis and documentation of radar images and their associated targets in a menu-driven, user oriented environment.

Cross-instrument Analysis Correlation Software

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

McJunkin, Timothy R.

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

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

NASA Astrophysics Data System (ADS)

Geske, Dagmar; Hess, Robert

1998-09-01

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

Assuring NASA's Safety and Mission Critical Software

NASA Technical Reports Server (NTRS)

Deadrick, Wesley

2015-01-01

What is IV&V? Independent Verification and Validation (IV&V) is an objective examination of safety and mission critical software processes and products. Independence: 3 Key parameters: Technical Independence; Managerial Independence; Financial Independence. NASA IV&V perspectives: Will the system's software: Do what it is supposed to do?; Not do what it is not supposed to do?; Respond as expected under adverse conditions?. Systems Engineering: Determines if the right system has been built and that it has been built correctly. IV&V Technical Approaches: Aligned with IEEE 1012; Captured in a Catalog of Methods; Spans the full project lifecycle. IV&V Assurance Strategy: The IV&V Project's strategy for providing mission assurance; Assurance Strategy is driven by the specific needs of an individual project; Implemented via an Assurance Design; Communicated via Assurance Statements.

A test matrix sequencer for research test facility automation

NASA Technical Reports Server (NTRS)

Mccartney, Timothy P.; Emery, Edward F.

1990-01-01

The hardware and software configuration of a Test Matrix Sequencer, a general purpose test matrix profiler that was developed for research test facility automation at the NASA Lewis Research Center, is described. The system provides set points to controllers and contact closures to data systems during the course of a test. The Test Matrix Sequencer consists of a microprocessor controlled system which is operated from a personal computer. The software program, which is the main element of the overall system is interactive and menu driven with pop-up windows and help screens. Analog and digital input/output channels can be controlled from a personal computer using the software program. The Test Matrix Sequencer provides more efficient use of aeronautics test facilities by automating repetitive tasks that were once done manually.

MATHEMATICAL METHODS IN MEDICAL IMAGE PROCESSING

PubMed Central

ANGENENT, SIGURD; PICHON, ERIC; TANNENBAUM, ALLEN

2013-01-01

In this paper, we describe some central mathematical problems in medical imaging. The subject has been undergoing rapid changes driven by better hardware and software. Much of the software is based on novel methods utilizing geometric partial differential equations in conjunction with standard signal/image processing techniques as well as computer graphics facilitating man/machine interactions. As part of this enterprise, researchers have been trying to base biomedical engineering principles on rigorous mathematical foundations for the development of software methods to be integrated into complete therapy delivery systems. These systems support the more effective delivery of many image-guided procedures such as radiation therapy, biopsy, and minimally invasive surgery. We will show how mathematics may impact some of the main problems in this area, including image enhancement, registration, and segmentation. PMID:23645963

Evaluation of Software for Introducing Protein Structure: Visualization and Simulation

ERIC Educational Resources Information Center

White, Brian; Kahriman, Azmin; Luberice, Lois; Idleh, Farhia

2010-01-01

Communicating an understanding of the forces and factors that determine a protein's structure is an important goal of many biology and biochemistry courses at a variety of levels. Many educators use computer software that allows visualization of these complex molecules for this purpose. Although visualization is in wide use and has been associated…

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)

PubMed Central

Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, Isaac

2010-01-01

Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases (“data marts”) can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software. PMID:20190053

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

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.

A dose-response curve for biodosimetry from a 6 MV electron linear accelerator

PubMed Central

Lemos-Pinto, M.M.P.; Cadena, M.; Santos, N.; Fernandes, T.S.; Borges, E.; Amaral, A.

2015-01-01

Biological dosimetry (biodosimetry) is based on the investigation of radiation-induced biological effects (biomarkers), mainly dicentric chromosomes, in order to correlate them with radiation dose. To interpret the dicentric score in terms of absorbed dose, a calibration curve is needed. Each curve should be constructed with respect to basic physical parameters, such as the type of ionizing radiation characterized by low or high linear energy transfer (LET) and dose rate. This study was designed to obtain dose calibration curves by scoring of dicentric chromosomes in peripheral blood lymphocytes irradiated in vitro with a 6 MV electron linear accelerator (Mevatron M, Siemens, USA). Two software programs, CABAS (Chromosomal Aberration Calculation Software) and Dose Estimate, were used to generate the curve. The two software programs are discussed; the results obtained were compared with each other and with other published low LET radiation curves. Both software programs resulted in identical linear and quadratic terms for the curve presented here, which was in good agreement with published curves for similar radiation quality and dose rates. PMID:26445334

Surface-tension phenomena in organismal biology: an introduction to the symposium.

PubMed

Bourouiba, Lydia; Hu, David L; Levy, Rachel

2014-12-01

Flows driven by surface tension are both ubiquitous and diverse, involving the drinking of birds and bees, the flow of xylem in plants, the impact of raindrops on animals, respiration in humans, and the transmission of diseases in plants and animals, including humans. The fundamental physical principles underlying such flows provide a unifying framework to interpret the adaptations of the microorganisms, animals, and plants that rely upon them. The symposium on "Surface-Tension Phenomena in Organismal Biology" assembled an interdisciplinary group of researchers to address a large spectrum of topics, all articulated around the role of surface tension in shaping biology, health, and ecology. The contributions to the symposium and the papers in this issue are meant to be a starting point for novices to familiarize themselves with the fundamentals of flows driven by surface tension; to understand how they can play a governing role in many settings in organismal biology; and how such understanding of nature's use of surface tension can, in turn, inspire humans to innovate. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Biological aerosol background characterization

NASA Astrophysics Data System (ADS)

Blatny, Janet; Fountain, Augustus W., III

2011-05-01

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

TEACHING "MATH-LITE" CONSERVATION (BOOK REVIEW OF CONSERVATION BIOLOGY WITH RAMAS ECOLAB)

EPA Science Inventory

This book is designed to serve as a laboratory workbook for an undergraduate course in conservation biology, environmental science, or natural resource management. By integrating with RAMAS EcoLab software, the book provides instructors with hands-on computer exercises that can ...

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks.

PubMed

Wu, Siqi; Joseph, Antony; Hammonds, Ann S; Celniker, Susan E; Yu, Bin; Frise, Erwin

2016-04-19

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set ofDrosophilaearly embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation ofDrosophilaexpression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. The performance of PP with theDrosophiladata suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

A capillary-driven micromixer: idea and fabrication

NASA Astrophysics Data System (ADS)

Lee, Chun-Te; Lee, Chun-Che

2012-10-01

Microfluidic systems have been drawing attention upon the various branches of engineering science and the allied areas within biology and biomedicine. In this paper, a fabrication of a capillary-driven micromixer using photoresist JSR and glasses is proposed. We design three types of planar capillary-driven micormixers with different sizes of baffles in the channel. Flow tests have shown that the micromixer with a baffle gap of 100 μm and space of 100 μm reaches a best mixing performance of 93% in gray-level image analysis.

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

PubMed

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

2012-08-01

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

Strategic directions of computing at Fermilab

NASA Astrophysics Data System (ADS)

Wolbers, Stephen

1998-05-01

Fermilab computing has changed a great deal over the years, driven by the demands of the Fermilab experimental community to record and analyze larger and larger datasets, by the desire to take advantage of advances in computing hardware and software, and by the advances coming from the R&D efforts of the Fermilab Computing Division. The strategic directions of Fermilab Computing continue to be driven by the needs of the experimental program. The current fixed-target run will produce over 100 TBytes of raw data and systems must be in place to allow the timely analysis of the data. The collider run II, beginning in 1999, is projected to produce of order 1 PByte of data per year. There will be a major change in methodology and software language as the experiments move away from FORTRAN and into object-oriented languages. Increased use of automation and the reduction of operator-assisted tape mounts will be required to meet the needs of the large experiments and large data sets. Work will continue on higher-rate data acquisition systems for future experiments and projects. R&D projects will be pursued as necessary to provide software, tools, or systems which cannot be purchased or acquired elsewhere. A closer working relation with other high energy laboratories will be pursued to reduce duplication of effort and to allow effective collaboration on many aspects of HEP computing.

ISEES: an institute for sustainable software to accelerate environmental science

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

PubMed

Sosinsky, G E; Baker, T S; Hand, G; Ellisman, M H

1999-01-01

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise. Copyright 1999 Academic Press.

BioBrick assembly standards and techniques and associated software tools.

PubMed

Røkke, Gunvor; Korvald, Eirin; Pahr, Jarle; Oyås, Ove; Lale, Rahmi

2014-01-01

The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.

The path to enlightenment: making sense of genomic and proteomic information.

PubMed

Maurer, Martin H

2004-05-01

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.

Designing and encoding models for synthetic biology.

PubMed

Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

2009-08-06

A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.

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

PubMed

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

2016-01-01

Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ∼5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and administered concurrently to all students. New exam questions were developed using Bloom's taxonomy, and exam results were analyzed statistically with validated assessment tools. All but the comprehensive final exam were returned to students for self-evaluation and remediation. Among other approaches, course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters. Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 72.9% (2010) to 83.5% (2015). Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions. Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20% increase in the course pass rates over time, also for the high-risk population. These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention, particularly for our academically at-risk students. © 2016 M. C. Carmichael et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

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

PubMed Central

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

2013-01-01

Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats. Availability and implementation: All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials. Contact: stg@inf.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23329415

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

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

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

Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.

PubMed

Fertig, Elana J; Stein-O'Brien, Genevieve; Jaffe, Andrew; Colantuoni, Carlo

2014-01-01

Patterns in time-course gene expression data can represent the biological processes that are active over the measured time period. However, the orthogonality constraint in standard pattern-finding algorithms, including notably principal components analysis (PCA), confounds expression changes resulting from simultaneous, non-orthogonal biological processes. Previously, we have shown that Markov chain Monte Carlo nonnegative matrix factorization algorithms are particularly adept at distinguishing such concurrent patterns. One such matrix factorization is implemented in the software package CoGAPS. We describe the application of this software and several technical considerations for identification of age-related patterns in a public, prefrontal cortex gene expression dataset.

Design Automation in Synthetic Biology.

PubMed

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

2017-04-03

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

Discovering objects in a blood recipient information system.

PubMed

Qiu, D; Junghans, G; Marquardt, K; Kroll, H; Mueller-Eckhardt, C; Dudeck, J

1995-01-01

Application of object-oriented (OO) methodologies has been generally considered as a solution to the problem of improving the software development process and managing the so-called software crisis. Among them, object-oriented analysis (OOA) is the most essential and is a vital prerequisite for the successful use of other OO methodologies. Though there are already a good deal of OOA methods published, the most important aspect common to all these methods: discovering objects classes truly relevant to the given problem domain, has remained a subject to be intensively researched. In this paper, using the successful development of a blood recipient information system as an example, we present our approach which is based on the conceptual framework of responsibility-driven OOA. In the discussion, we also suggest that it may be inadequate to simply attribute the software crisis to the waterfall model of the software development life-cycle. We are convinced that the real causes for the failure of some software and information systems should be sought in the methodologies used in some crucial phases of the software development process. Furthermore, a software system can also fail if object classes essential to the problem domain are not discovered, implemented and visualized, so that the real-world situation cannot be faithfully traced by it.

Software For Design Of Life-Support Systems

NASA Technical Reports Server (NTRS)

Rudokas, Mary R.; Cantwell, Elizabeth R.; Robinson, Peter I.; Shenk, Timothy W.

1991-01-01

Design Assistant Workstation (DAWN) computer program is prototype of expert software system for analysis and design of regenerative, physical/chemical life-support systems that revitalize air, reclaim water, produce food, and treat waste. Incorporates both conventional software for quantitative mathematical modeling of physical, chemical, and biological processes and expert system offering user stored knowledge about materials and processes. Constructs task tree as it leads user through simulated process, offers alternatives, and indicates where alternative not feasible. Also enables user to jump from one design level to another.

Swarming Robot Design, Construction and Software Implementation

NASA Technical Reports Server (NTRS)

Stolleis, Karl A.

2014-01-01

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

Software and resources for computational medicinal chemistry

PubMed Central

Liao, Chenzhong; Sitzmann, Markus; Pugliese, Angelo; Nicklaus, Marc C

2011-01-01

Computer-aided drug design plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on structure-based drug design, ligand-based drug design, chemical databases and chemoinformatics tools. PMID:21707404

Model-Driven Development for scientific computing. An upgrade of the RHEEDGr program

NASA Astrophysics Data System (ADS)

Daniluk, Andrzej

2009-11-01

Model-Driven Engineering (MDE) is the software engineering discipline, which considers models as the most important element for software development, and for the maintenance and evolution of software, through model transformation. Model-Driven Architecture (MDA) is the approach for software development under the Model-Driven Engineering framework. This paper surveys the core MDA technology that was used to upgrade of the RHEEDGR program to C++0x language standards. New version program summaryProgram title: RHEEDGR-09 Catalogue identifier: ADUY_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUY_v3_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 21 263 No. of bytes in distributed program, including test data, etc.: 1 266 982 Distribution format: tar.gz Programming language: Code Gear C++ Builder Computer: Intel Core Duo-based PC Operating system: Windows XP, Vista, 7 RAM: more than 1 MB Classification: 4.3, 7.2, 6.2, 8, 14 Does the new version supersede the previous version?: Yes Nature of problem: Reflection High-Energy Electron Diffraction (RHEED) is a very useful technique for studying growth and surface analysis of thin epitaxial structures prepared by the Molecular Beam Epitaxy (MBE). The RHEED technique can reveal, almost instantaneously, changes either in the coverage of the sample surface by adsorbates or in the surface structure of a thin film. Solution method: The calculations are based on the use of a dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface. Reasons for new version: Responding to the user feedback the graphical version of the RHEED program has been upgraded to C++0x language standards. Also, functionality and documentation of the program have been improved. Summary of revisions: Model-Driven Architecture (MDA) is the approach defined by the Object Management Group (OMG) for software development under the Model-Driven Engineering framework [1]. The MDA approach shifts the focus of software development from writing code to building models. By adapting a model-centric approach, the MDA approach hopes to automate the generation of system implementation artifacts directly from the model. The following three models are the core of the MDA: (i) the Computation Independent Model (CIM), which is focused on basic requirements of the system, (ii) the Platform Independent Model (PIM), which is used by software architects and designers, and is focused on the operational capabilities of a system outside the context of a specific platform, and (iii) the Platform Specific Model (PSM), which is used by software developers and programmers, and includes details relating to the system for a specific platform. Basic requirements for the calculation of the RHEED intensity rocking curves in the one-beam condition have been described in Ref. [2]. Fig. 1 shows the PIM for the present version of the program. Fig. 2 presents the PSM for the program. The TGraph2D.bpk package has been recompiled to Graph2D0x.bpl and upgraded according to C++0x language standards. Fig. 3 shows the PSM of the Graph2D component, which is manifested by the Graph2D0x.bpl package presently. This diagram is a graphic presentation of the static view, which shows a collection of declarative model elements and their relationships. Installation instructions of the Graph2D0x package can be found in the new distribution. The program requires the user to provide the appropriate parameters for the crystal structure under investigation. These parameters are loaded from the parameters.ini file at run-time. Instructions for the preparation of the .ini files can be found in the new distribution. The program enables carrying out one-dimensional dynamical calculations for the fcc lattice, with a two-atoms basis and fcc lattice, with one atom basis but yet the zeroth Fourier component of the scattering potential in the TRHEED1D::crystPotUg() function can be modified according to users' specific application requirements. A graphical user interface (GUI) for the program has been reconstructed. The program has been compiled with English/USA regional and language options. Unusual features: The program is distributed in the form of main projects RHEEDGr_09.cbproj and Graph2D0x.cbproj with associated files, and should be compiled using Code Gear C++ Builder 2009 compilers. Running time: The typical running time is machine and user-parameters dependent. References: OMG, Model Driven Architecture Guide Version 1.0.1, 2003, http://www.omg.org/cgi-bin/doc?omg/03-06-01. A. Daniluk, Comput. Phys. Comm. 166 (2005) 123.

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

PubMed

Karabatsos, George

2017-02-01

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

A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks.

PubMed

Browne, Fiona; Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

2010-03-01

This study applied a knowledge-driven data integration framework for the inference of protein-protein interactions (PPI). Evidence from diverse genomic features is integrated using a knowledge-driven Bayesian network (KD-BN). Receiver operating characteristic (ROC) curves may not be the optimal assessment method to evaluate a classifier's performance in PPI prediction as the majority of the area under the curve (AUC) may not represent biologically meaningful results. It may be of benefit to interpret the AUC of a partial ROC curve whereby biologically interesting results are represented. Therefore, the novel application of the assessment method referred to as the partial ROC has been employed in this study to assess predictive performance of PPI predictions along with calculating the True positive/false positive rate and true positive/positive rate. By incorporating domain knowledge into the construction of the KD-BN, we demonstrate improvement in predictive performance compared with previous studies based upon the Naive Bayesian approach. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2016-01-01

High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance. DOI: http://dx.doi.org/10.7554/eLife.10047.001 PMID:26840049

Process-driven and biological characterisation and mapping of seabed habitats sensitive to trawling.

PubMed

Foveau, Aurélie; Vaz, Sandrine; Desroy, Nicolas; Kostylev, Vladimir E

2017-01-01

The increase of anthropogenic pressures on the marine environment together with the necessity of a sustainable management of marine living resources have underlined the need to map and model coastal environments, particularly for the purposes of spatial planning and for the implementation of integrated ecosystem-based management approach. The present study compares outputs of a process-driven benthic habitat sensitivity (PDS) model to the structure, composition and distribution of benthic invertebrates in the Eastern English Channel and southern part of the North Sea. Trawl disturbance indicators (TDI) computed from species biological traits and benthic community composition were produced from samples collected with a bottom trawl. The TDI was found to be highly correlated to the PDS further validating the latter's purpose to identify natural process-driven pattern of sensitivity. PDS was found to reflect an environmental potential that may no longer be fully observable in the field and difference with in situ biological observations could be partially explained by the spatial distribution of fishery pressure on the seafloor. The management implication of these findings are discussed and we suggest that, used in conjunction with TDI approaches, PDS may help monitor management effort by evaluating the difference between the current state and the presumed optimal environmental status of marine benthic habitats.

Process-driven and biological characterisation and mapping of seabed habitats sensitive to trawling

PubMed Central

Desroy, Nicolas; Kostylev, Vladimir E.

2017-01-01

The increase of anthropogenic pressures on the marine environment together with the necessity of a sustainable management of marine living resources have underlined the need to map and model coastal environments, particularly for the purposes of spatial planning and for the implementation of integrated ecosystem-based management approach. The present study compares outputs of a process-driven benthic habitat sensitivity (PDS) model to the structure, composition and distribution of benthic invertebrates in the Eastern English Channel and southern part of the North Sea. Trawl disturbance indicators (TDI) computed from species biological traits and benthic community composition were produced from samples collected with a bottom trawl. The TDI was found to be highly correlated to the PDS further validating the latter’s purpose to identify natural process-driven pattern of sensitivity. PDS was found to reflect an environmental potential that may no longer be fully observable in the field and difference with in situ biological observations could be partially explained by the spatial distribution of fishery pressure on the seafloor. The management implication of these findings are discussed and we suggest that, used in conjunction with TDI approaches, PDS may help monitor management effort by evaluating the difference between the current state and the presumed optimal environmental status of marine benthic habitats. PMID:28981504

Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities.

PubMed

Quo, Chang F; Kaddi, Chanchala; Phan, John H; Zollanvari, Amin; Xu, Mingqing; Wang, May D; Alterovitz, Gil

2012-07-01

Recent advances in high-throughput biotechnologies have led to the rapid growing research interest in reverse engineering of biomolecular systems (REBMS). 'Data-driven' approaches, i.e. data mining, can be used to extract patterns from large volumes of biochemical data at molecular-level resolution while 'design-driven' approaches, i.e. systems modeling, can be used to simulate emergent system properties. Consequently, both data- and design-driven approaches applied to -omic data may lead to novel insights in reverse engineering biological systems that could not be expected before using low-throughput platforms. However, there exist several challenges in this fast growing field of reverse engineering biomolecular systems: (i) to integrate heterogeneous biochemical data for data mining, (ii) to combine top-down and bottom-up approaches for systems modeling and (iii) to validate system models experimentally. In addition to reviewing progress made by the community and opportunities encountered in addressing these challenges, we explore the emerging field of synthetic biology, which is an exciting approach to validate and analyze theoretical system models directly through experimental synthesis, i.e. analysis-by-synthesis. The ultimate goal is to address the present and future challenges in reverse engineering biomolecular systems (REBMS) using integrated workflow of data mining, systems modeling and synthetic biology.

Computational challenges in modeling gene regulatory events.

PubMed

Pataskar, Abhijeet; Tiwari, Vijay K

2016-10-19

Cellular transcriptional programs driven by genetic and epigenetic mechanisms could be better understood by integrating "omics" data and subsequently modeling the gene-regulatory events. Toward this end, computational biology should keep pace with evolving experimental procedures and data availability. This article gives an exemplified account of the current computational challenges in molecular biology.

To drive or be driven: the path of a mouse model of recurrent pregnancy loss.

PubMed Central

Bonney, Elizabeth A.; Brown, Stephen A.

2015-01-01

This review is an example of the use of an animal model to try to understand the immune biology of pregnancy. A well-known model of recurrent spontaneous pregnancy loss is put in clinical, historical and theoretical context, with emphasis on T cell biology. PMID:24472815

Making Microscopy Motivating, Memorable, & Manageable for Undergraduate Students with Digital Imaging Laboratories

ERIC Educational Resources Information Center

Weeks, Andrea; Bachman. Beverly; Josway, Sarah; North, Brittany; Tsuchiya, Mirian T.N.

2013-01-01

Microscopy and precise observation are essential skills that are challenging to teach effectively to large numbers of undergraduate biology students. We implemented student-driven digital imaging assignments for microscopy in a large enrollment laboratory for organismal biology. We detail how we promoted student engagement with the material and…

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

PubMed Central

Kunz, Manfred; Vera, Julio; Wolkenhauer, Olaf

2013-01-01

MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. To demonstrate the application of this approach, we adopt it to investigate mechanisms of collective repression on p21 by multiple miRNAs. We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts. PMID:24350286

A Comparative Evaluation of Videodiscs for General Biology.

ERIC Educational Resources Information Center

Ralph, Charles L.

1995-01-01

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

Scalable computing for evolutionary genomics.

PubMed

Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

2012-01-01

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project, BioNode encourages creating free and open source VM images, for multiple targets, through one central project. BioNode can be deployed on Windows, OSX, Linux, and in the Cloud. Next to the downloadable BioNode images, we provide tutorials online, which empower bioinformaticians to install and run BioNode in different environments, as well as information for future initiatives, on creating and building such images.

Multibiodose radiation emergency triage categorization software.

PubMed

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

2014-07-01

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

Advances in systems biology: computational algorithms and applications.

PubMed

Huang, Yufei; Zhao, Zhongming; Xu, Hua; Shyr, Yu; Zhang, Bing

2012-01-01

The 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) was held on April 22-24, 2012 in Nashville, Tennessee, USA. The conference featured six technical sessions, one tutorial session, one workshop, and 3 keynote presentations that covered state-of-the-art research activities in genomics, systems biology, and intelligent computing. In addition to a major emphasis on the next generation sequencing (NGS)-driven informatics, ICIBM 2012 aligned significant interests in systems biology and its applications in medicine. We highlight in this editorial the selected papers from the meeting that address the developments of novel algorithms and applications in systems biology.

Model-Driven Development of Interactive Multimedia Applications with MML

NASA Astrophysics Data System (ADS)

Pleuss, Andreas; Hussmann, Heinrich

There is an increasing demand for high-quality interactive applications which combine complex application logic with a sophisticated user interface, making use of individual media objects like graphics, animations, 3D graphics, audio or video. Their development is still challenging as it requires the integration of software design, user interface design, and media design.

Educational JavaBeans: a Requirements Driven Architecture.

ERIC Educational Resources Information Center

Hall, Jon; Rapanotti, Lucia

This paper investigates, through a case study, the development of a software architecture that is compatible with a system's high-level requirements. The case study is an example of an extended customer/supplier relationship (post-point of sale support) involved in e-universities and is representative of a class of enterprise without current…

Solving Common Mathematical Problems

NASA Technical Reports Server (NTRS)

Luz, Paul L.

2005-01-01

Mathematical Solutions Toolset is a collection of five software programs that rapidly solve some common mathematical problems. The programs consist of a set of Microsoft Excel worksheets. The programs provide for entry of input data and display of output data in a user-friendly, menu-driven format, and for automatic execution once the input data has been entered.

Tools to Ease Your Internet Adventures: Part I.

ERIC Educational Resources Information Center

Descy, Don E.

1993-01-01

This first of a two-part series highlights three tools that improve accessibility to Internet resources: (1) Alex, a database that accesses files in FTP (file transfer protocol) sites; (2) Archie, software that searches for file names with a user's search term; and (3) Gopher, a menu-driven program to access Internet sites. (LRW)

A Software Hub for High Assurance Model-Driven Development and Analysis

DTIC Science & Technology

2007-01-23

verification of UML models in TLPVS. In Thomas Baar, Alfred Strohmeier, Ana Moreira, and Stephen J. Mellor, editors, UML 2004 - The Unified Modeling...volume 3785 of Lecture Notes in Computer Science, pages 52–65, Manchester, UK, Nov 2005. Springer. [GH04] Günter Graw and Peter Herrmann. Transformation

Dare to Share

ERIC Educational Resources Information Center

Briggs, Linda L.

2007-01-01

Today, as difficult as it is for large institutions to keep software and hardware up-to-date, the challenge and expense of keeping up is only amplified for smaller colleges and universities. In the area of data-driven decision-making (DDD), the challenge can be even greater. Because smaller schools are pressed for time and resources on nearly all…

Effects of Response-Driven Feedback in Computer Science Learning

ERIC Educational Resources Information Center

Fernandez Aleman, J. L.; Palmer-Brown, D.; Jayne, C.

2011-01-01

This paper presents the results of a project on generating diagnostic feedback for guided learning in a first-year course on programming and a Master's course on software quality. An online multiple-choice questions (MCQs) system is integrated with neural network-based data analysis. Findings about how students use the system suggest that the…

Colaborated Architechture Framework for Composition UML 2.0 in Zachman Framework

NASA Astrophysics Data System (ADS)

Hermawan; Hastarista, Fika

2016-01-01

Zachman Framework (ZF) is the framework of enterprise architechture that most widely adopted in the Enterprise Information System (EIS) development. In this study, has been developed Colaborated Architechture Framework (CAF) to collaborate ZF with Unified Modeling Language (UML) 2.0 modeling. The CAF provides the composition of ZF matrix that each cell is consist of the Model Driven architechture (MDA) from the various UML models and many Software Requirement Specification (SRS) documents. Implementation of this modeling is used to develops Enterprise Resource Planning (ERP). Because ERP have a coverage of applications in large numbers and complexly relations, it is necessary to use Agile Model Driven Design (AMDD) approach as an advanced method to transforms MDA into components of application modules with efficiently and accurately. Finally, through the using of the CAF, give good achievement in fullfilment the needs from all stakeholders that are involved in the overall process stage of Rational Unified Process (RUP), and also obtaining a high satisfaction to fullfiled the functionality features of the ERP software in PT. Iglas (Persero) Gresik.

Working with the HL7 metamodel in a Model Driven Engineering context.

PubMed

Martínez-García, A; García-García, J A; Escalona, M J; Parra-Calderón, C L

2015-10-01

HL7 (Health Level 7) International is an organization that defines health information standards. Most HL7 domain information models have been designed according to a proprietary graphic language whose domain models are based on the HL7 metamodel. Many researchers have considered using HL7 in the MDE (Model-Driven Engineering) context. A limitation has been identified: all MDE tools support UML (Unified Modeling Language), which is a standard model language, but most do not support the HL7 proprietary model language. We want to support software engineers without HL7 experience, thus real-world problems would be modeled by them by defining system requirements in UML that are compliant with HL7 domain models transparently. The objective of the present research is to connect HL7 with software analysis using a generic model-based approach. This paper introduces a first approach to an HL7 MDE solution that considers the MIF (Model Interchange Format) metamodel proposed by HL7 by making use of a plug-in developed in the EA (Enterprise Architect) tool. Copyright © 2015 Elsevier Inc. All rights reserved.

A Verification-Driven Approach to Traceability and Documentation for Auto-Generated Mathematical Software

NASA Technical Reports Server (NTRS)

Denney, Ewen W.; Fischer, Bernd

2009-01-01

Model-based development and automated code generation are increasingly used for production code in safety-critical applications, but since code generators are typically not qualified, the generated code must still be fully tested, reviewed, and certified. This is particularly arduous for mathematical and control engineering software which requires reviewers to trace subtle details of textbook formulas and algorithms to the code, and to match requirements (e.g., physical units or coordinate frames) not represented explicitly in models or code. Both tasks are complicated by the often opaque nature of auto-generated code. We address these problems by developing a verification-driven approach to traceability and documentation. We apply the AUTOCERT verification system to identify and then verify mathematical concepts in the code, based on a mathematical domain theory, and then use these verified traceability links between concepts, code, and verification conditions to construct a natural language report that provides a high-level structured argument explaining why and how the code uses the assumptions and complies with the requirements. We have applied our approach to generate review documents for several sub-systems of NASA s Project Constellation.

Linking Goal-Oriented Requirements and Model-Driven Development

NASA Astrophysics Data System (ADS)

Pastor, Oscar; Giachetti, Giovanni

In the context of Goal-Oriented Requirement Engineering (GORE) there are interesting modeling approaches for the analysis of complex scenarios that are oriented to obtain and represent the relevant requirements for the development of software products. However, the way to use these GORE models in an automated Model-Driven Development (MDD) process is not clear, and, in general terms, the translation of these models into the final software products is still manually performed. Therefore, in this chapter, we show an approach to automatically link GORE models and MDD processes, which has been elaborated by considering the experience obtained from linking the i * framework with an industrially applied MDD approach. The linking approach proposed is formulated by means of a generic process that is based on current modeling standards and technologies in order to facilitate its application for different MDD and GORE approaches. Special attention is paid to how this process generates appropriate model transformation mechanisms to automatically obtain MDD conceptual models from GORE models, and how it can be used to specify validation mechanisms to assure the correct model transformations.

Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

PubMed

Chakrabortty, S; Sen, M; Pal, P

2014-03-01

A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

Automated glycopeptide analysis—review of current state and future directions

PubMed Central

Dallas, David C.; Martin, William F.; Hua, Serenus

2013-01-01

Glycosylation of proteins is involved in immune defense, cell–cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural analysis of glycoproteins—glycoproteomics—remains in its infancy due to the scarcity of high-throughput analytical platforms capable of determining glycopeptide composition and structure, especially platforms for complex biological mixtures. Glycopeptide composition and structure can be determined with high mass-accuracy mass spectrometry, particularly when combined with chromatographic separation, but the sheer volume of generated data necessitates computational software for interpretation. This review discusses the current state of glycopeptide assignment software—advances made to date and issues that remain to be addressed. The various software and algorithms developed so far provide important insights into glycoproteomics. However, there is currently no freely available software that can analyze spectral data in batch and unambiguously determine glycopeptide compositions for N- and O-linked glycopeptides from relevant biological sources such as human milk and serum. Few programs are capable of aiding in structural determination of the glycan component. To significantly advance the field of glycoproteomics, analytical software and algorithms are required that: (i) solve for both N- and O-linked glycopeptide compositions, structures and glycosites in biological mixtures; (ii) are high-throughput and process data in batches; (iii) can interpret mass spectral data from a variety of sources and (iv) are open source and freely available. PMID:22843980

Bigdata Driven Cloud Security: A Survey

NASA Astrophysics Data System (ADS)

Raja, K.; Hanifa, Sabibullah Mohamed

2017-08-01

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

Modeling and simulation of biological systems using SPICE language

PubMed Central

Lallement, Christophe; Haiech, Jacques

2017-01-01

The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology). PMID:28787027

Comparing the Impacts of Tutorial and Edutainment Software Programs on Students' Achievements, Misconceptions, and Attitudes towards Biology

ERIC Educational Resources Information Center

Kara, Yilmaz; Yesilyurt, Selami

2008-01-01

The purpose of this study was to investigate the effects of tutorial and edutainment design of instructional software programs related to the "cell division" topic on student achievements, misconceptions and attitudes. An experimental research design including the cell division achievement test (CAT), the cell division concept test (CCT) and…

Biological Impact of Music and Software-Based Auditory Training

ERIC Educational Resources Information Center

Kraus, Nina

2012-01-01

Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals--both young and old--encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in…

Modeling Mendel's Laws on Inheritance in Computational Biology and Medical Sciences

ERIC Educational Resources Information Center

Singh, Gurmukh; Siddiqui, Khalid; Singh, Mankiran; Singh, Satpal

2011-01-01

The current research article is based on a simple and practical way of employing the computational power of widely available, versatile software MS Excel 2007 to perform interactive computer simulations for undergraduate/graduate students in biology, biochemistry, biophysics, microbiology, medicine in college and university classroom setting. To…

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

DTIC Science & Technology

2007-01-01

15 4.2.3. Users of Systems for Combating Biological Warfare ................................ 16 4.2.4...21 4.3.1. Existing Biosurveillance Systems .............................................................. 22 4.3.2. Automatic Integration...74 6.4.4. Multi-Agent System Management System (MMS).................................... 75 6.4.5. Agent Glossary

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Design of a Knowledge Driven HIS

PubMed Central

Pryor, T. Allan; Clayton, Paul D.; Haug, Peter J.; Wigertz, Ove

1987-01-01

Design of the software architecture for a knowledge driven HIS is presented. In our design the frame has been used as the basic unit of knowledge representation. The structure of the frame is being designed to be sufficiently universal to contain knowledge required to implement not only expert systems, but almost all traditional HIS functions including ADT, order entry and results review. The design incorporates a two level format for the knowledge. The first level as ASCII records is used to maintain the knowledge base while the second level converted by special knowledge compilers to standard computer languages is used for efficient implementation of the knowledge applications.

Clinical Note Creation, Binning, and Artificial Intelligence

PubMed Central

Deliberato, Rodrigo Octávio; Stone, David J

2017-01-01

The creation of medical notes in software applications poses an intrinsic problem in workflow as the technology inherently intervenes in the processes of collecting and assembling information, as well as the production of a data-driven note that meets both individual and healthcare system requirements. In addition, the note writing applications in currently available electronic health records (EHRs) do not function to support decision making to any substantial degree. We suggest that artificial intelligence (AI) could be utilized to facilitate the workflows of the data collection and assembly processes, as well as to support the development of personalized, yet data-driven assessments and plans. PMID:28778845

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

PubMed Central

Le Novère, Nicolas; Hucka, Michael; Anwar, Nadia; Bader, Gary D; Demir, Emek; Moodie, Stuart; Sorokin, Anatoly

2011-01-01

The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner. PMID:22180826

Modular design of synthetic gene circuits with biological parts and pools.

PubMed

Marchisio, Mario Andrea

2015-01-01

Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

PubMed

Le Novère, Nicolas; Hucka, Michael; Anwar, Nadia; Bader, Gary D; Demir, Emek; Moodie, Stuart; Sorokin, Anatoly

2011-11-30

The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner.

Biopathways representation and simulation on hybrid functional petri net.

PubMed

Matsuno, Hiroshi; Tanaka, Yukiko; Aoshima, Hitoshi; Doi, Atsushi; Matsui, Mika; Miyano, Satoru

2011-01-01

The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.

Group Support Systems (GSS)

NASA Technical Reports Server (NTRS)

Hamel, Gary P.; Wijesinghe, R.

1996-01-01

Groupware is a term describing an emerging computer software technology enhancing the ability of people to work together as a group, (a software driven 'group support system'). This project originated at the beginning of 1992 and reports were issued describing the activity through May 1995. These reports stressed the need for process as well as technology. That is, while the technology represented a computer assisted method for groups to work together, the Group Support System (GSS) technology als required an understanding of the facilitation process electronic meetings demand. Even people trained in traditional facilitation techniques did not necessarily aimlessly adopt groupware techniques. The latest phase of this activity attempted to (1) improve the facilitation process by developing training support for a portable groupware computer system, and (2) to explore settings and uses for the portable groupware system using different software, such as Lotus Notes.

Development and evaluation of a Fault-Tolerant Multiprocessor (FTMP) computer. Volume 2: FTMP software

NASA Technical Reports Server (NTRS)

Lala, J. H.; Smith, T. B., III

1983-01-01

The software developed for the Fault-Tolerant Multiprocessor (FTMP) is described. The FTMP executive is a timer-interrupt driven dispatcher that schedules iterative tasks which run at 3.125, 12.5, and 25 Hz. Major tasks which run under the executive include system configuration control, flight control, and display. The flight control task includes autopilot and autoland functions for a jet transport aircraft. System Displays include status displays of all hardware elements (processors, memories, I/O ports, buses), failure log displays showing transient and hard faults, and an autopilot display. All software is in a higher order language (AED, an ALGOL derivative). The executive is a fully distributed general purpose executive which automatically balances the load among available processor triads. Provisions for graceful performance degradation under processing overload are an integral part of the scheduling algorithms.

Domain specific software architectures: Command and control

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Integrating interactive computational modeling in biology curricula.

PubMed

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

2015-03-01

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

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy.

PubMed

Matsuda, Atsushi; Schermelleh, Lothar; Hirano, Yasuhiro; Haraguchi, Tokuko; Hiraoka, Yasushi

2018-05-15

Correction of chromatic shift is necessary for precise registration of multicolor fluorescence images of biological specimens. New emerging technologies in fluorescence microscopy with increasing spatial resolution and penetration depth have prompted the need for more accurate methods to correct chromatic aberration. However, the amount of chromatic shift of the region of interest in biological samples often deviates from the theoretical prediction because of unknown dispersion in the biological samples. To measure and correct chromatic shift in biological samples, we developed a quadrisection phase correlation approach to computationally calculate translation, rotation, and magnification from reference images. Furthermore, to account for local chromatic shifts, images are split into smaller elements, for which the phase correlation between channels is measured individually and corrected accordingly. We implemented this method in an easy-to-use open-source software package, called Chromagnon, that is able to correct shifts with a 3D accuracy of approximately 15 nm. Applying this software, we quantified the level of uncertainty in chromatic shift correction, depending on the imaging modality used, and for different existing calibration methods, along with the proposed one. Finally, we provide guidelines to choose the optimal chromatic shift registration method for any given situation.

BiNA: A Visual Analytics Tool for Biological Network Data

PubMed Central

Gerasch, Andreas; Faber, Daniel; Küntzer, Jan; Niermann, Peter; Kohlbacher, Oliver; Lenhof, Hans-Peter; Kaufmann, Michael

2014-01-01

Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA - the Biological Network Analyzer - a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/. PMID:24551056

Computational challenges in modeling gene regulatory events

PubMed Central

Pataskar, Abhijeet; Tiwari, Vijay K.

2016-01-01

ABSTRACT Cellular transcriptional programs driven by genetic and epigenetic mechanisms could be better understood by integrating “omics” data and subsequently modeling the gene-regulatory events. Toward this end, computational biology should keep pace with evolving experimental procedures and data availability. This article gives an exemplified account of the current computational challenges in molecular biology. PMID:27390891

Terrestrial Slugs as a Model Organism for Inquiry-Based Experimentation in a Majors General Biology Laboratory

ERIC Educational Resources Information Center

Peters, Brenda J.; Blair, Amy C.

2013-01-01

Many biology educators at the undergraduate level are revamping their laboratory curricula to incorporate inquiry-based research experiences so that students can directly participate in the process of science and improve their scientific reasoning skills. Slugs are an ideal organism for use in such a student-directed, hypothesis-driven experience.…

Quantitative evaluation of software packages for single-molecule localization microscopy.

PubMed

Sage, Daniel; Kirshner, Hagai; Pengo, Thomas; Stuurman, Nico; Min, Junhong; Manley, Suliana; Unser, Michael

2015-08-01

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB(®) graphical user interface.

PubMed

Sridhar, Vishnu B; Tian, Peifang; Dale, Anders M; Devor, Anna; Saisan, Payam A

2014-01-01

We present a database client software-Neurovascular Network Explorer 1.0 (NNE 1.0)-that uses MATLAB(®) based Graphical User Interface (GUI) for interaction with a database of 2-photon single-vessel diameter measurements from our previous publication (Tian et al., 2010). These data are of particular interest for modeling the hemodynamic response. NNE 1.0 is downloaded by the user and then runs either as a MATLAB script or as a standalone program on a Windows platform. The GUI allows browsing the database according to parameters specified by the user, simple manipulation and visualization of the retrieved records (such as averaging and peak-normalization), and export of the results. Further, we provide NNE 1.0 source code. With this source code, the user can database their own experimental results, given the appropriate data structure and naming conventions, and thus share their data in a user-friendly format with other investigators. NNE 1.0 provides an example of seamless and low-cost solution for sharing of experimental data by a regular size neuroscience laboratory and may serve as a general template, facilitating dissemination of biological results and accelerating data-driven modeling approaches.