ebTrack: an environmental bioinformatics system built upon ArrayTrack™

ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis and interpretation of environmental and toxicological data from diverse sources. It is based on enhancements to the US FDA developed ArrayTrack™ system through additional analysis modules for gene expression data as well as through incorporation and linkages to modules for analysis of proteomic and metabonomic datasets that include tandem mass spectra. ebTrack uses a client-server architecture with the free and open source PostgreSQL as its database engine, and java tools for user interface, analysis, visualization, and web-based deployment. Several predictive tools that are critical for environmental health research are currently supported in ebTrack, including Significance Analysis of Microarray (SAM). Furthermore, new tools are under continuous integration, and interfaces to environmental health risk analysis tools are being developed in order to make ebTrack widely usable. These health risk analysis tools include the Modeling ENvironment for TOtal Risk studies (MENTOR) for source-to-dose exposure modeling and the DOse Response Information ANalysis system (DORIAN) for health outcome modeling. The design of ebTrack is presented in detail and steps involved in its application are summarized through an illustrative application

Isolated Open Rotor Noise Prediction Assessment Using the F31A31 Historical Blade Set

In an effort to mitigate next-generation fuel efficiency and environmental impact concerns for aviation, open rotor propulsion systems have received renewed interest. However, maintaining the high propulsive efficiency while simultaneously meeting noise goals has been one of the challenges in making open rotor propulsion a viable option. Improvements in prediction tools and design methodologies have opened the design space for next generation open rotor designs that satisfy these challenging objectives. As such, validation of aerodynamic and acoustic prediction tools has been an important aspect of open rotor research efforts. This paper describes validation efforts of a combined computational fluid dynamics and Ffowcs Williams and Hawkings equation methodology for open rotor aeroacoustic modeling. Performance and acoustic predictions were made for a benchmark open rotor blade set and compared with measurements over a range of rotor speeds and observer angles. Overall, the results indicate that the computational approach is acceptable for assessing low-noise open rotor designs. Additionally, this approach may be used to provide realistic incident source fields for acoustic shielding/scattering studies on various aircraft configurations

Carbon Footprint Estimation Tool for Residential Buildings for Non-Specialized Users: OERCO2 Project

Existing tools for environmental certification of buildings are failing in their ability to reach the general public and to create social awareness, since they require not only specialized knowledge regarding construction and energy sources, but also environmental knowledge. In this paper, an open-source online tool for the estimation of the carbon footprint of residential buildings by non-specialized users is presented as a product from the OERCO2 Erasmus + project. The internal calculations, data management and operation of this tool are extensively explained. The ten most common building typologies built in the last decade in Spain are analysed by using the OERCO2 tool, and the order of magnitude of the results is analysed by comparing them to the ranges determined by other authors. The OERCO2 tool proves itself to be reliable, with its results falling within the defined logical value ranges. Moreover, the major simplification of the interface allows non-specialized users to evaluate the sustainability of buildings. Further research is oriented towards its inclusion in other environmental certification tools and in Building Information Modeling (BIM) environments

Development and Implementation of Dynamic Scripts to Execute Cycled WRF/GSI Forecasts

Automating the coupling of data assimilation (DA) and modeling systems is a unique challenge in the numerical weather prediction (NWP) research community. In recent years, the Development Testbed Center (DTC) has released well-documented tools such as the Weather Research and Forecasting (WRF) model and the Gridpoint Statistical Interpolation (GSI) DA system that can be easily downloaded, installed, and run by researchers on their local systems. However, developing a coupled system in which the various preprocessing, DA, model, and postprocessing capabilities are all integrated can be labor-intensive if one has little experience with any of these individual systems. Additionally, operational modeling entities generally have specific coupling methodologies that can take time to understand and develop code to implement properly. To better enable collaborating researchers to perform modeling and DA experiments with GSI, the Short-term Prediction Research and Transition (SPoRT) Center has developed a set of Perl scripts that couple GSI and WRF in a cycling methodology consistent with the use of real-time, regional observation data from the National Centers for Environmental Prediction (NCEP)/Environmental Modeling Center (EMC). Because Perl is open source, the code can be easily downloaded and executed regardless of the user's native shell environment. This paper will provide a description of this open-source code and descriptions of a number of the use cases that have been performed by SPoRT collaborators using the scripts on different computing systems

Web portal on environmental sciences "ATMOS''

International audienceThe developed under INTAS grant web portal ATMOS (http://atmos.iao.ru and http://atmos.scert.ru) makes available to the international research community, environmental managers, and the interested public, a bilingual information source for the domain of Atmospheric Physics and Chemistry, and the related application domain of air quality assessment and management. It offers access to integrated thematic information, experimental data, analytical tools and models, case studies, and related information and educational resources compiled, structured, and edited by the partners into a coherent and consistent thematic information resource. While offering the usual components of a thematic site such as link collections, user group registration, discussion forum, news section etc., the site is distinguished by its scientific information services and tools: on-line models and analytical tools, and data collections and case studies together with tutorial material. The portal is organized as a set of interrelated scientific sites, which addressed basic branches of Atmospheric Sciences and Climate Modeling as well as the applied domains of Air Quality Assessment and Management, Modeling, and Environmental Impact Assessment. Each scientific site is open for external access information-computational system realized by means of Internet technologies. The main basic science topics are devoted to Atmospheric Chemistry, Atmospheric Spectroscopy and Radiation, Atmospheric Aerosols, Atmospheric Dynamics and Atmospheric Models, including climate models. The portal ATMOS reflects current tendency of Environmental Sciences transformation into exact (quantitative) sciences and is quite effective example of modern Information Technologies and Environmental Sciences integration. It makes the portal both an auxiliary instrument to support interdisciplinary projects of regional environment and extensive educational resource in this important domain

The OpenESEA Modeling Language and Tool for Ethical, Social, and Environmental Accounting

Assessing business operations’ ethical, social, and environmental impacts is a key practice for establishing sustainable development. There is a multitude of methods that describes how to perform such assessments. Often these methods are supported by an ICT tool. In most cases, the tools are developed to support a single method only and do not allow any tailoring. Therefore, they are rigid and inflexible. In this article, we present a novel model-driven approach for alleviating managerial issues that arise as a consequence of the complex landscape of ethical, social, and environmental accounting methods and tools. We have developed an open-source, model-driven tool, called openESEA. OpenESEA parses and interprets textual models, that are specified according to a domain-specific language (DSL). We have performed another iteration of the DSL engineering process, which is in line with the design science paradigm. We have validated the new DSL version by means of a user study. As a result, we present a new version of the openESEA modeling language and interpreter. The results of the user study with regards to performance, perceived usefulness, and perceived ease of use of modeling language are encouraging and provide us with a basis to continue developing new versions with more functionalities. The contributions of this work include a new version of the modeling language, a new version of the interpreter, knowledge surrounding the development of these artifacts, and a protocol for evaluating the quality of textual DSLs. The modeling language and interpreter are relevant for sustainability practitioners and consultants since our tool support has the potential to reduce redundancy in ethical, social, and environmental accounting. Our work is valuable to researchers that aim to assess and reduce the complexity of their modeling languages

The Community Simulator: A Python package for microbial ecology

Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.Comment: 14 pages, 6 figure

Joining participatory approach and spatially-based modelling tools for groundwater resource management.

Although a lot of science has been produced on Water Resource Management (WRM) in the Information and Communication Technology (ICT) sector, WRM is still poorly addressed via scientific means. Some reasons for this may be: the underrated importance given to this topic at political and decision-making level; the low-capacity of the research environment to transfer results; and missing numerical modelling capacities at agencies and governing authorities. ICT may provide tools for water planning and management, as discussed within the ICT4WATER cluster initiative. Among these, GIS-integrated numerical modeling is a robust method to represent hydrological systems and to provide answers to problems of protection of groundwater resources. Because these tools require a high level of knowledge pertaining to various disciplines, they are often disregarded as complex “tricky games” providing unrealistic results. This is a barrier to the uptake of technologies for water management. To overcome this issue, the application of ICT tools has been combined with an innovative participatory approach, and large capacity building activities, in the framework of the H2020 FREEWAT project (FREE and open source software tools for WATer resource management; www.freewat.eu). The major result of the project consists in an open source and public domain, QGIS-integrated modeling platform for promoting WRM. FREEWAT capabilities have been demonstrated at 14 case studies in EU and non-EU Countries, where the effectiveness of few measures foreseen in River Basin Management Plans for achieving good status of water bodies was tested. At each case study, a Focus Group (FG) participated by local stakeholders (e.g., river basin authorities, research institutions, environmental protection agencies, environmental associations) was formed and seven meetings were organized. During these meetings, the objective of each case study, the methodology to be adopted, including definition of the conceptual model and of data needed, were discussed. The FG also took decisions on scenarios to be simulated for testing the feasibility of the foreseen measures. FGs aimed at demonstrating that WRM may be performed with open source and public domain software and participants’ perception on using ICT tools for WRM was discussed. Some of the implemented models are now being used for operational purposes: Vrbansky plato (Slovenia), where FREEWAT is used to monitor remediation of heating oil spillage and the water supply company intends to maintain and use developed groundwater flow model for managed groundwater recharge with induced riverbank filtration; the Bremerhaven case study (Germany), where the local water authority intends to use the developed groundwater flow model for predictions; the Scarlino-Follonica case study (Italy), where the model will be used by the regional authority to manage private groundwater remediation projects in a large industrial contaminated site; the Gozo case study (Malta), where the model is being developed to support the assessment of good groundwater quantitative status as part of the implementation of the Water Framework Directive

Building Energy Modeling with OpenStudio : A Practical Guide for Students and Professionals

The energy, environmental, and societal challenges of the twenty-first century are here; they are crystal clear; and they are daunting. Our responses to those challenges are less clear, but one component at least is obvious—we need a better building stock, one that uses less energy, provides greater comfort and security, and houses and supports the economic activity of a rapidly growing and urbanizing population. One of the most powerful tools in our collective belts is building energy modeling (BEM), physics-based software simulation of building energy use given a description of the physical building, its use patterns, and prevailing weather conditions. BEM is a sine qua non tool for designing and operating buildings to the levels of energy efficiency that our future and present require. According to the AIA 2030 Commitment report, buildings designed using BEM use 20% less energy than those designed without it. BEM is also instrumental in developing and updating the codes, standards, certificates, and financial incentive infrastructure that supports energy efficiency in all building projects, including those that don’t directly use BEM. The OpenStudio project has been a driving force in the evolution of BTO’s BEM program. OpenStudio was BTO’s first truly open-source software project, a strategic direction that has influenced BTO’s entire BEM portfolio. Open-source is not an altruistic emergent enterprise. Successful open-source projects are funded, centrally managed, and resemble proprietary software projects in many structural and operational ways. Source control. Code reviews. Regression testing. Bug reporting and fixing. Pre-feature documentation. Post-feature documentation. The full Monty