Logic Modeling and the Ridiculome Under the Rug

Logic-derived modeling has been used to map biological networks and to study arbitrary functional interactions, and fine-grained kinetic modeling can accurately predict the detailed behavior of well-characterized molecular systems; at present, however, neither approach comes close to unraveling the full complexity of a cell. The current data revolution offers significant promises and challenges to both approaches - and could bring them together as it has spurred the development of new methods and tools that may help to bridge the many gaps between data, models, and mechanistic understanding. Have you used logic modeling in your research? It would not be surprising if many biologists would answer no to this hypothetical question. And it would not be true. In high school biology we already became familiar with cartoon diagrams that illustrate basic mechanisms of the molecular machinery operating inside cells. These are nothing else but simple logic models. If receptor and ligand are present, then receptor-ligand complexes form; if a receptor-ligand complex exists, then an enzyme gets activated; if the enzyme is active, then a second messenger is being produced; and so on. Such chains of causality are the essence of logic models (Figure 1a). Arbitrary events and mechanisms are abstracted; relationships are simplified and usually involve just two possible conditions and three possible consequences. The presence or absence of one or more molecule, activity, or function, [some icons in the cartoon] will determine whether another one of them will be produced (created, up-regulated, stimulated) [a \u27positive\u27 link] or destroyed (degraded, down-regulated, inhibited) [a \u27negative\u27 link], or be unaffected [there is no link]. The icons and links often do not follow a standardized format, but when we look at such a cartoon diagram, we believe that we \u27understand\u27 how the system works. Because our brain is easily able to process these relationships, these diagrams allow us to answer two fundamental types of questions related to the system: why (are certain things happening)? What if (we make some changes)

Воспитание пациентов по поводу восприятия качества медицинских услуг

This study was conducted to decrease the difference in the perception of health assistance quality between patients and medical personnel. That investigations developed an analysis on how preceptions of this problem are formed by medical personnel and patients, an elaboration of the model of the logarithm of the perception, and a program with new methods of patient education. This decreased tensionand motivated the medical personnel to solve the problems and increase the quality of the health assistance. That investigation solved many of the expectancies of the population, patients and formed a medicine directioned to a patients needs.Наша работа поставила перед собой цель объяснить поступление множества жалоб на качество медицинских услуг путем анализа способности восприятия качества медицинских услуг пациентами, населением и медицинскими работниками, так как множество тяжелых заболеваний, не имеющих позитивное разрешение, могут быть объяснены как некачественное медицинское обслуживание. Результаты анализа позволили нам узнать логику мышления пациентов и медработников, разработать модель восприятия качества и программу воспитания с целью правильного понимания, как пациентами, так и медработниками своей роли в достижения выздоровления

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results: In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined

WTC2005-64171 LOBATTO POINT QUADRATURE FOR THERMAL LUBRICATION PROBLEMS INVOLVING COMPRESSIBLE LUBRICANTS

ABSTRACT Refined solutions of thermal lubrication problems generally require fine mesh and many iteration steps. To resolve these difficulties, Elrod and Brewe (1) proposed an efficient algorithm based on the use of Lobatto point quadrature. Within this approach, the unknown temperature across the film is written in a series of Legendre polynomials. This paper presents a Lobatto point quadrature algorithm which is applicable for thermal lubrication problems with compressible lubricants. In this case both density and viscosity of the lubricant are taken to be temperature and pressure dependent. The transverse velocity is obtained from the continuity equation. Use of the Labatto point calculation method has resulted in greater accuracy without the use of a large number of grid points INTRODUCTION Accurate solutions of thermal lubrication problems employ discretization both across the film thickness and along the other directions of the fluid domain. Intensive numerical integration across the film is usually required. Improving the calculation of this integration can further reduce the computational time. One of the fastest procedures is Gauss open integration, which employs the optimal collocation of the integration points (usually at the zeros of various types of Jacobi polynomials). Moreover, function representation in series of orthogonal polynomials with collocation over these grid points offers improved interpolation (2). However, the classical Gaussian quadrature is "open", i.e., the ends of the integrals are not used. For differential equations, the end points correspond to the boundary points, so they have to be included in the quadrature. Therefore, the application of Gaussian integration within the solution of PDEs requires the use of the Lobatto point version of the Gauss schem

Three-Phase Phase-Shifting Transformer with Regulation in Neutral Point

The paper aimed to research mode characteristics of phase shift installation based on one three-phase transformer having three windings. Usually, such installations are two cores: exciting transformer and regulation transformer. In paper the installation functional scheme description, as well main relations which determine currents and voltages character in scheme elements during regulation process are given. It is shown, that installation is able to provide phase shift angle regulation up to . The installation scheme is designed to place the control module in the neutral connection point of regulation windings. Such solution allowing essential reduction of installation rated capacity compare to traditional one and excluding necessity of special isolation of shell. Proposed solution ensure in such mode compact construction and commodity for transportation, mounting and service