Supplementary Documentation Research Articles

Programmatic access to logical models in the Cell Collective modeling environment via a REST API

SummaryCell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. Availability and implementationThe Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective (http://thecellcollective.org). Contactthelikar2@unl.edu. Supplementary informationTechnical user documentation: https://goo.gl/U52GWo.

USE OF EPORTFOLIO TOOL FOR REFLECTION IN ENGINEERING DESIGN

Electronic portfolios (ePortfolios) can be a beneficial tool to facilitate student learning, evaluate learning outcomes and showcase skills and experience. At the University of Guelph, the School of Engineering piloted the use of ePortfolios within the third year design course of the engineering design sequence of courses. With the implementation of graduate attributes by the CEAB, more “soft skill” attributes like individual and teamwork, project management, and lifelong learning are important skills developed by students within the design courses and can be assessed within an ePortfolio environment.Students submitted guided reflections related to major deliverables within the course. The reflections were assessed for the level of insight through rubrics in the learning management system. Overall, students improved their ability to reflect and provided good insight into their learning and roles within their group project. The response to the reflections by students was mixed. Many students found value in reflecting on their experience while other students were frustrated by the method of filling the reflection form.In the future, the objectives for reflection should be made clearer with supplementary documentation to the lecture material. Adjusting the timing of the reflections to correspond to less stressful periods of the semester and improving the ePortfolio process will help with student engagement.

MEMGENE: Spatial pattern detection in genetic distance data

Summary Landscape genetics studies using neutral markers have focused on the relationship between gene flow and landscape features. Spatial patterns in the genetic distances among individuals may reflect spatially uneven patterns of gene flow caused by landscape features that influence movement and dispersal. We present a method and software for identifying spatial neighbourhoods in genetic distance data that adopts a regression framework where the predictors are generated using Moran's eigenvectors maps (MEM), a multivariate technique developed for spatial ecological analyses and recommended for genetic applications. Using simulated genetic data, we show that our MEMGENE method can recover patterns reflecting the landscape features that influenced gene flow. We also apply MEMGENE to genetic data from a highly vagile ungulate population and demonstrate spatial genetic neighbourhoods aligned with a river likely to reduce, but not eliminate, gene flow. We developed the MEMGENE package for R in order to detect and visualize relatively weak or cryptic spatial genetic patterns and aid researchers in generating hypotheses about the ecological processes that may underlie these patterns. MEMGENE provides a flexible set of R functions that can be used to modify the analysis. Detailed supplementary documentation and tutorials are provided.

Supplementary Historical Documents

Supplementary Historical Documents

Supplementary Documents for Russell’s Logic, 1905–08

A philosopher may develop ideas on his or her own or follow them in the works of others. Different kinds of documentary threads will develop. Historians of a subject may follow either kind. In the period of Toward “Principia Mathematica”, 1905–08, Russell engaged with developments in the writings of Poincaré, Haldane, Schiller and Berry, among others. What follows are remarks on supplementary documents (one being on-line) for a fuller study of logical and philosophical threads in the period.

SPINAL: scalable protein interaction network alignment

Given protein-protein interaction (PPI) networks of a pair of species, a pairwise global alignment corresponds to a one-to-one mapping between their proteins. Based on the presupposition that such a mapping provides pairs of functionally orthologous proteins accurately, the results of the alignment may then be used in comparative systems biology problems such as function prediction/verification or construction of evolutionary relationships. We show that the problem is NP-hard even for the case where the pair of networks are simply paths. We next provide a polynomial time heuristic algorithm, SPINAL, which consists of two main phases. In the first coarse-grained alignment phase, we construct all pairwise initial similarity scores based on pairwise local neighborhood matchings. Using the produced similarity scores, the fine-grained alignment phase produces the final one-to-one mapping by iteratively growing a locally improved solution subset. Both phases make use of the construction of neighborhood bipartite graphs and the contributors as a common primitive. We assess the performance of our algorithm on the PPI networks of yeast, fly, human and worm. We show that based on the accuracy measures used in relevant work, our method outperforms the state-of-the-art algorithms. Furthermore, our algorithm does not suffer from scalability issues, as such accurate results are achieved in reasonable running times as compared with the benchmark algorithms. Supplementary Document, open source codes, useful scripts, all the experimental data and the results are freely available at http://code.google.com/p/spinal/. Supplementary data are available at Bioinformatics online.

MDA Development in Manufacturing Execution System by UML and Supplementary Document

In this paper, we propose evaluation and verification about the MDA development by UML which aims at the improvement in productivity and maintainability of MES. We consider why MDA (Model Driven Architecture) is not widely spread in the development of MES (Manufacturing Execution System) and propose a method to overcome the problem which prevents the developers of MES from adopting MDA. The method makes it possible to apply the MDA development with UML (Unified Modeling Language) to the development of MES by introducing additional documents to supplement. We evaluated the proposed method by using the prototype system which was developed with a UML modeling tool and Excel macros. The application of the system to a practical example showed that the proposed method required about half number of documents and software development workers of the conventional one. It is expected that the MDA development of MES with UML and the proposed supplemental documents encourage the reuse of the documents and the productivity and the maintainability are remarkably improved.

Allelematch: an R package for identifying unique multilocus genotypes where genotyping error and missing data may be present

We present allelematch, an R package, to automate the identification of unique multilocus genotypes in data sets where the number of individuals is unknown, and where genotyping error and missing data may be present. Such conditions commonly occur in noninvasive sampling protocols. Output from the software enables a comparison of unique genotypes and their matches, and facilitates the review of differences between profiles. The software has a variety of applications in molecular ecology, and may be valuable where a large number of samples must be processed, unique genotypes identified, and repeated observations made over space and time. We used simulations to assess the performance of allelematch and found that it can reliably and accurately determine the correct number of unique genotypes (± 3%) across a broad range of data set properties. We found that the software performs with highest accuracy when genotyping error is below 4%. The R package is available from the Comprehensive R Archive Network (http://cran.r-project.org/). Supplementary documentation and tutorials are provided.

Truthing gap: imagining a relational geography of the uninhabitable

During 2008–10, I was the Artist in Residence of the Leverhulme Trust, at the National Oceanography Centre, (NOCS), Southampton, working with sonar geophysicist Dr Tim Le Bas, exploring methods of seabed mapping and undersea survey. During this period I documented aspects of oceanographic study, learnt processes used by my scientific colleagues, conducted performative interventions and made works in direct response to the context of NOCS. The work produced was shown at an exhibition at University of Wales Institute, Cardiff in 2009 and will be developed into a larger exhibition at the John Hansard Gallery, Southampton in 2012. This article constitutes both a re-presentation of my primary research and a reflection on the methods I adopted to address the issues raised by my inquiries. Works produced are both referred to directly and represented via supplementary documentation.

SU‐E‐I‐83: Filling the Gap: Using Detailed Machine Parameters to Refine Skin Dose Calculations for Fluoroscopic Sentinel Events

Purpose: To examine the role that detailed machine logs, supplementary procedural documentation and vendor‐generated technique and dosimetry information can play in refining calculation of peak skin dose for sentinel event investigations.Methods: Vendor‐specific machine logs, skin‐dose estimations, and procedural observations can supplement the fluoroscopic times and air kerma values that all fluoroscopic machines are required to report since 2006. Information available from vendors varies considerably, and in some cases specific application products must be purchased to access this information. Information embodied may include table position, c‐arm geometry, collimation, individual run and fluoro acquisition dosimetry, technique factors (mA, kVp, pulse configuration), mode of operation and other data. Peak skin dose estimates based on HIS/RIS data and DICOM image headers were compared to calculations supplemented by the detailed machine logs and vendor dosimetry estimates. Skin dose maps were generated from air kerma readings and from the DICOM information associated with each run. Assumptions are necessary in this approach to apportion the fluoroscopic contribution, which can be 80% of the air kerma. Corresponding skin dose maps were generated with inclusion of more detailed machine log data and the resulting peak skin dose location and magnitudes were compared.Results: Significant deviations were observed between peak skin dose calculations based on DICOM information alone with attendant assumptions versus those obtained with more detailed machine log data. Detailed logs provide complementary information that replaces assumptions on fluoroscopic dose contributions with more reliable values. Conclusions: Additional information from vendorˈs logs and dose‐ estimates and from other sources can increase the confidence in skin‐dose calculations, but the specific assumptions made by both the physicist and the vendor in making such estimates must be carefully examined. The comparison enables the stand‐alone assumptions to be validated and also allows evaluation of vendor dosimetry estimates.

Italy – Tax Audits to Identify Fictitious Corporate Residence

The need for a tax audit in the area of fictitious residence derives from circumstantial evidence – acquired during the intelligence phase – or from other clues that may have emerged during inspection. Further to the cognizance gathered within an enterprise’s operative context, investigations aim at the research of accounting, supplementary, and electronic documentation. Such investigations may turn out to be particularly complex as they are generally required to consider the distinctive characteristics of international relations, the specificity of the subject matter, as well as the various jurisdictions (and legislatures) involved. Inspectors are bound to have their operations comply to a rather structured power-duties system, within which the respect of the taxpayer’s rights acquires particular relevance.

The causes of food waste in the supplier–retailer interface: Evidences from the UK and Spain

Food and drink waste is a significant problem for economic, environmental and food security reasons. Government efforts have focused on diverting waste away from landfill through regulation, taxation and public awareness. However, efforts to understand why waste occurs have been limited, particularly in the interface between retailers and suppliers. This research aims to address this problem by identifying the main root causes of waste in the supplier–retailer interface.The research is exploratory in nature as there is a paucity of studies focusing on food waste across the supply chain. Data were collected through 43 interviews with managers in food manufacturing, wholesaling and retailing in two countries: the UK (24) and Spain (19). Data from the interviews and supplementary documentation were analyzed using causal maps. This approach helped to identify the main root causes of waste which were categorized into three groups: (1) mega-trends in the marketplace, (2) natural causes related to the products and processes, and (3) management root causes on which practitioners have a direct impact.The paper discusses the root causes of food waste and good practices identified from the interviews. Differences between the UK and Spain are discussed, presenting potential learning opportunities for practitioners in these countries and highlighting opportunities for further research.

Automated manipulation of systems biology models using libSBML within Taverna workflows

Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. This selection is stored as an XML file which enables Taverna to present the subset of the API for use in the composition of workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as a SBML model. Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net

Spanish methodological approach for biosphere assessment of radioactive waste disposal

The development of radioactive waste disposal facilities requires implementation of measures that will afford protection of human health and the environment over a specific temporal frame that depends on the characteristics of the wastes. The repository design is based on a multi-barrier system: (i) the near-field or engineered barrier, (ii) far-field or geological barrier and (iii) the biosphere system. Here, the focus is on the analysis of this last system, the biosphere. A description is provided of conceptual developments, methodological aspects and software tools used to develop the Biosphere Assessment Methodology in the context of high-level waste (HLW) disposal facilities in Spain. This methodology is based on the BIOMASS "Reference Biospheres Methodology" and provides a logical and systematic approach with supplementary documentation that helps to support the decisions necessary for model development. It follows a five-stage approach, such that a coherent biosphere system description and the corresponding conceptual, mathematical and numerical models can be built. A discussion on the improvements implemented through application of the methodology to case studies in international and national projects is included. Some facets of this methodological approach still require further consideration, principally an enhanced integration of climatology, geography and ecology into models considering evolution of the environment, some aspects of the interface between the geosphere and biosphere, and an accurate quantification of environmental change processes and rates.

Patterns of global terrorism, 1985-2005: U.S. Department of State reports with supplementary documents and statistics

Patterns of Global Terrorism: US Department of State Reports with Supplementary Documents and Statistics is arranged in a user-friendly format replete with tables, graphs, and illustrative material - much of it from the original reports but with additional material developed by Berkshire and its editors (and clearly indicated as additional content). This reference set is an essential resource for every college, school, and public library. A full, comprehensive index guides readers, and summary definitions, chronologies, and year-to-year comparisons provide broad context. Fifteen related government documents are integrated to provide context and to give readers a sense of the debates, past and present, about global terrorism. Never before published in book form, these documents provide the most complete and authoritative historical data on terrorism around the globe.

BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network

BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray datasets with missing data. To evaluate the statistical features of generated Bayesian networks, re-sampling procedures are utilized to yield collections of candidate 1st-order network sets for mining dense coherent sub-networks. The R package and the supplementary documentation are available at http://www.cls.zju.edu.cn/binfo/BNArray/.

Patterns of Global Terrorism 1985‐2005: US Department of State Reports with Supplementary Documents and Statistics

Patterns of Global Terrorism 1985‐2005: US Department of State Reports with Supplementary Documents and Statistics

A macroion electrokinetics algorithm

A numerical algorithm is presented for the standard model of macroion electrokinetics and certain generalizations of it. The macroion consists of a cylindrical section with identical, hemispheroidal endcaps, each piece having arbitrary length. The system of one macroion and adjoining salt solution is subjected to an arbitrary sequence of pulsed electrical fields and pulsed translational and rotational velocities. Numerical solutions are obtained for the time dependent electrostatic and mobile ion concentration fields and the solvent velocity. From these fields the dielectric response, force, and torque are calculated. Generalizations of the standard model include the diffusive motion of macroion surface charges, partial slip of solvent motion at the macroion surface, and a simple model for the reactive exchange of surface charge with solution ions. The primary illustrative application is to recent measurements of electric birefringence versus applied field frequency for poly-(tetrafluorothylene) colloidal particles, but a few results are presented for the dielectric response of DNA fragments and of spherical colloidal particles. The source code and additional details are provided as supplementary documentation.

Quick Screen for Voice and Supplementary Documents for Identifying Pediatric Voice Disorders

Quick Screen for Voice and Supplementary Documents for Identifying Pediatric Voice Disorders

Quick Screen for Voice and Supplementary Documents for Identifying Pediatric Voice Disorders

Three documents are provided to help the speech-language pathologist (SLP) identify children with voice disorders and educate family members. The first is a quickly administered screening test that covers multiple aspects of voice, respiration, and resonance. It was tested on 3000 children in kindergarten and first and fifth grades, and on 47 preschoolers. The second document is a checklist of functional indicators of voice disorders that could be given to parents, teachers, or other caregivers to increase their attention to potential causes of voice problems and to provide the SLP with information pertinent to identification. The final document is a brochure with basic information about voice disorders and the need for medical examination. It may be used to help the SLP educate parents, particularly about the need for laryngeal examination for children who have been identified as having a voice problem.