Issues of shaping the students’ professional and terminological competence in science area of expertise in the sustainable development era

The paper deals with the problem of future biology teachers’ vocational preparation process and shaping in them of those capacities that contribute to the conservation and enhancement of our planet’s biodiversity as a reflection of the leading sustainable development goals of society. Such personality traits are viewed through the prism of forming the future biology teachers’ professional and terminological competence. The main aspects and categories that characterize the professional and terminological competence of future biology teachers, including terminology, nomenclature, term, nomen and term element, have been explained. The criteria and stages of shaping the future biology teachers’ professional and terminological competence during the vocational training process have been fixed. Methods, techniques, technologies, guiding principles and forms of staged work on the forming of an active terminological dictionary of students have been described and specified. The content of the distant special course “Latin. Botanical Terminology”, which provides training for future teachers to study the professional subjects and to understand of international scientific terminology, has been presented. It is concluded that the proper level of formation of the future biology teachers’ professional and terminological competence will eventually ensure the qualitative preparation of pupils for life in a sustainable development era

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

Mapping Big Data into Knowledge Space with Cognitive Cyber-Infrastructure

Big data research has attracted great attention in science, technology, industry and society. It is developing with the evolving scientific paradigm, the fourth industrial revolution, and the transformational innovation of technologies. However, its nature and fundamental challenge have not been recognized, and its own methodology has not been formed. This paper explores and answers the following questions: What is big data? What are the basic methods for representing, managing and analyzing big data? What is the relationship between big data and knowledge? Can we find a mapping from big data into knowledge space? What kind of infrastructure is required to support not only big data management and analysis but also knowledge discovery, sharing and management? What is the relationship between big data and science paradigm? What is the nature and fundamental challenge of big data computing? A multi-dimensional perspective is presented toward a methodology of big data computing.Comment: 59 page

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c

Big Data Visualization Tools

Data visualization is the presentation of data in a pictorial or graphical format, and a data visualization tool is the software that generates this presentation. Data visualization provides users with intuitive means to interactively explore and analyze data, enabling them to effectively identify interesting patterns, infer correlations and causalities, and supports sense-making activities.Comment: This article appears in Encyclopedia of Big Data Technologies, Springer, 201

Emerging from the MIST: A Connector Tool for Supporting Programming by Non-programmers

Software development is an iterative process. As user re-quirements emerge software applications must be extended to support the new requirements. Typically, a programmer will add new code to an existing code base of an application to provide a new functionality. Previous research has shown that such extensions are easier when application logic is clearly separated from the user interface logic. Assuming that a programmer is already familiar with the existing code base, the task of writing the new code can be considered to be split into two sub-tasks: writing code for the application logic; that is, the actual functionality of the application; and writing code for the user interface that will expose the functionality to the end user. The goal of this research is to reduce the effort required to create a user interface once the application logic has been created, toward supporting scientists with minimal pro-gramming knowledge to be able to create and modify pro-grams. Using a Model View Controller based architecture, various model components which contain the application logic can be built and extended. The process of creating and extending the views (user interfaces) on these model components is simplified through the use of our Malleable Interactive Software Toolkit (MIST), a tool set an infrastructure intended to simplify the design and extension of dynamically reconfigurable interfaces. This paper focuses on one tool in the MIST suite, a connec-tor tool that enables the programmer to evolve the user interface as the application logic evolves by connecting related pieces of code together; either through simple drag-and-drop interactions or through the authoring of Python code. The connector tool exemplifies the types of tools in the MIST suite, which we expect will encourage collabora-tive development of applications by allowing users to inte-grate various components and minimizing the cost of de-veloping new user interfaces for the combined compo-nents