scholarly journals Developing a Coupling Model System of Global Rainfall Data and Open-Source Model for Water Forecast in Poorly Gauged Basins

2019 ◽  
Vol 3 (1) ◽  
pp. 355 ◽  
Author(s):  
Duong Du Bui ◽  
Duc Minh Tran ◽  
Huong Thi Vu ◽  
Nuong Thi Bui
Keyword(s):  
Open Source ◽  
Input Data ◽  
Water Security ◽  
Coupling Model ◽  
Source Model ◽  
Rainfall Data ◽  
Creative Commons ◽  
Set Up ◽  
User Friendly

Water security is under severe pressures from human interventions and climate change in all over the world and improved water forecast is essential for water management. HYPE is a semi-distributed hydrographic model, running on Windows or Linux operating systems. The code of the model is written by the Fortran programming language and open source as Lesser GNU Public License. HYPE has been becoming a widely used tool in the forecasting of transboundary flows. However, the application of HYPE encounters many difficulties in processing input data and serving the construction, calibration, and validation of the model. This article introduces the development of the V-HYPE tool that helps a couple of global rainfall data and HYPE model for operational use. V-HYPE allows developing a user-friendly interface and setting parameters of the HYPE model as well as evaluating errors and transforming and visually displaying the results of the model. Besides, the V-HYPE has the ability to show related maps (i.e. sub-basins, river network, lake, and dams, etc), set up input data, automatically download global rainfall data, and visually display results on WebGIS. V-HYPE also can generate bulletins supporting for operational water resources warning and forecasting works in Vietnam. The utilities of this tool are demonstrated in the case study of Serepok river basin.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium provided the original work is properly cited.

scholarly journals Comparing an insurer's perspective on building damages with modelled damages from pan-European winter windstorm event sets: a case study from Zurich, Switzerland

2021 ◽  
Vol 21 (1) ◽  
pp. 279-299
Author(s):  
Christoph Welker ◽  
Thomas Röösli ◽  
David N. Bresch
Keyword(s):  
Open Source ◽  
Return Period ◽  
Model Building ◽  
Information Service ◽  
Source Model ◽  
Insurance Companies ◽  
Risk Models ◽  
Risk Modelling ◽  
Modelling Approach

Abstract. With access to claims, insurers have a long tradition of being knowledge leaders on damages caused by windstorms. However, new opportunities have arisen to better assess the risks of winter windstorms in Europe through the availability of historic footprints provided by the Windstorm Information Service (Copernicus WISC). In this study, we compare how modelling of building damages complements claims-based risk assessment. We describe and use two windstorm risk models: an insurer's proprietary model and the open source CLIMADA platform. Both use the historic WISC dataset and a purposefully built, probabilistic hazard event set of winter windstorms across Europe to model building damages in the canton of Zurich, Switzerland. These approaches project a considerably lower estimate for the annual average damage (CHF 1.4 million), compared to claims (CHF 2.3 million), which originates mainly from a different assessment of the return period of the most damaging historic event Lothar–Martin. Additionally, the probabilistic modelling approach allows assessment of rare events, such as a 250-year-return-period windstorm causing CHF 75 million in damages, including an evaluation of the uncertainties. Our study emphasizes the importance of complementing a claims-based perspective with a probabilistic risk modelling approach to better understand windstorm risks. The presented open-source model provides a straightforward entry point for small insurance companies.

scholarly journals PALEOSTRIPv1.0 – a user-friendly 3D backtracking software to reconstruct paleo-bathymetries

2021 ◽  
Vol 14 (8) ◽  
pp. 5285-5305
Author(s):  
Florence Colleoni ◽  
Laura De Santis ◽  
Enrico Pochini ◽  
Edy Forlin ◽  
Riccardo Geletti ◽  
...  
Keyword(s):  
Open Source ◽  
Ocean Circulation ◽  
Ross Sea ◽  
Numerical Models ◽  
Physical Parameters ◽  
Sensitivity Tests ◽  
Drilling Site ◽  
User Friendly ◽  
2D And 3D

Abstract. Paleo-bathymetric reconstructions provide boundary conditions to numerical models of ice sheet evolution and ocean circulation that are critical to understanding their evolution through time. The geological community lacks a complex open-source tool that allows for community implementations and strengthens research synergies. To fill this gap, we present PALEOSTRIPv1.0, a MATLAB open-source software designed to perform 1D, 2D, and 3D backtracking of paleo-bathymetries. PALEOSTRIP comes with a graphical user interface (GUI) to facilitate computation of sensitivity tests and to allow the users to switch all the different processes on and off and thus separate the various aspects of backtracking. As such, all physical parameters can be modified from the GUI. It includes 3D flexural isostasy, 1D thermal subsidence, and possibilities to correct for prescribed sea level and dynamical topography changes. In the following, we detail the physics embedded within PALEOSTRIP, and we show its application using a drilling site (1D), a transect (2D), and a map (3D), taking the Ross Sea (Antarctica) as a case study. PALEOSTRIP has been designed to be modular and to allow users to insert their own implementations.

scholarly journals Comparing an insurer's perspective on building damages with modelled damages from pan-European winter windstorm event sets: a case study from Zurich, Switzerland

2020 ◽  
Author(s):  
Christoph Welker ◽  
Thomas Röösli ◽  
David N. Bresch
Keyword(s):  
Open Source ◽  
Return Period ◽  
Model Building ◽  
Information Service ◽  
Source Model ◽  
Insurance Companies ◽  
Risk Models ◽  
Risk Modelling ◽  
Modelling Approach

Abstract. With access to claims, insurers have a long tradition of being knowledge leaders on damages caused by e.g. windstorms. However, new opportunities have arisen to better assess the risks of winter windstorms in Europe through the availability of historic footprints provided by the Windstorm Information Service (Copernicus WISC). In this study, we compare how modelling of building damages complements claims-based risk assessment. We describe and use two windstorm risk models: the insurer's proprietary model and the open source CLIMADA platform. Both use the historic WISC dataset and a purposefully-built, probabilistic hazard event set of winter windstorms across Europe to model building damages in the canton of Zurich, Switzerland. These approaches project a considerably lower estimate for the annual average damage (CHF 1.4 million), compared to claims (CHF 2.3 million), which originates mainly from a different assessment of the return period of the most damaging historic event Lothar/Martin. Additionally, the probabilistic modelling approach allows assessing rare events, such as a 250-year return period windstorm causing CHF 75 million damages. Our study emphasises the importance of complementing a claims-based perspective with a probabilistic risk modelling approach to better understand windstorm risks. The presented open source model provides a straightforward entry point for small insurance companies.

Traffic Simulation with Open-Source and Commercial Traffic Microsimulators: A Case Study

2022 ◽  
Vol 24 (2) ◽  
pp. E49-E62
Author(s):  
Nelson Baza-Solares ◽  
Ruben Velasquez-Martínez ◽  
Cristian Torres-Bohórquez ◽  
Yerly Martínez-Estupiñán ◽  
Cristian Poliziani
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Transport Modeling ◽  
Graphical Interface ◽  
Urban Centers ◽  
Output Data ◽  
Computational Tools ◽  
Input And Output ◽  
User Friendly

The analysis of traffic problems in large urban centers often requires the use of computational tools, which give the possibility to make a more detailed analysis of the issue, suggest solutions, predict behaviors and, above all, support efficient decision-making. Transport microsimulation software programs are a handy set of tools for this type of analysis. This research paper shows a case study where functions and limitations of Aimsun version 8.2.0, a commercial-like European software and Sumo version 1.3.1, a European open-source software, are presented. The input and output data are similar in both software and the interpretation of results is quite intuitive for both, as well. However, Aimsun's graphical interface interprets results more user-friendly, because Sumo is an open-access software presented as an effective alternative tool for transport modeling.

scholarly journals NUMERICAL MODELING OF MORPHODYNAMIC CHANGES IN THE JADE ESTUARY – GERMANY

2011 ◽  
Vol 1 (32) ◽  
pp. 84 ◽  
Author(s):  
Almut Gelfort ◽  
Florian Ladage ◽  
Oliver Stoschek
Keyword(s):  
Numerical Modeling ◽  
Sediment Transport ◽  
Numerical Model ◽  
Input Data ◽  
Set Up

Based on a case study sediment transport was modeled numerically for the Jade estuary. Due to the construction of the JadeWeserPort the morphology in the area is undergoing a relocation. The study gives an overview on various studies undertaken as a consultant tool to help designers and decisions makers. A hydrodynamic as well as a morphodynamic numerical model was set up. Although the input data on the morphodynamic part was limited, the results showed that the tool at hand is capable of producing reliable results in the field of modeling sediment transport.

scholarly journals Runtime translation of OCL-like statements on Simulink models: Expanding domains and optimising queries

2021 ◽  
Author(s):  
Beatriz A. Sanchez ◽  
Athanasios Zolotas ◽  
Horacio Hoyos Rodriguez ◽  
Dimitris Kolovos ◽  
Richard F. Paige ◽  
...  
Keyword(s):  
Open Source ◽  
Source Model ◽  
Model Management ◽  
Management Framework ◽  
Domain Specific ◽  
Modelling Framework ◽  
Simulink Model ◽  
Alternative Approach ◽  
The Cost

AbstractOpen-source model management frameworks such as OCL and ATL tend to focus on manipulating models built atop the Eclipse Modelling Framework (EMF), a de facto standard for domain specific modelling. MATLAB Simulink is a widely used proprietary modelling framework for dynamic systems that is built atop an entirely different technical stack to EMF. To leverage the facilities of open-source model management frameworks with Simulink models, these can be transformed into an EMF-compatible representation. Downsides of this approach include the synchronisation of the native Simulink model and its EMF representation as they evolve; the completeness of the EMF representation, and the transformation cost which can be crippling for large Simulink models. We propose an alternative approach to bridge Simulink models with open-source model management frameworks that uses an “on-the-fly” translation of model management constructs into MATLAB statements. Our approach does not require an EMF representation and can mitigate the cost of the upfront transformation on large models. To evaluate both approaches we measure the performance of a model validation process with Epsilon (a model management framework) on a sample of large Simulink models available on GitHub. Our previous results suggest that, with our approach, the total validation time can be reduced by up to 80%. In this paper, we expand our approach to support the management of Simulink requirements and dictionaries, and we improve the approach to perform queries on collections of model elements more efficiently. We demonstrate the use of the Simulink requirements and dictionaries with a case study and we evaluate the optimisations on collection queries with an experiment that compares the performance of a set of queries on models with different sizes. Our results suggest an improvement by up to 99% on some queries.

scholarly journals Using Open Source Tools for Analysis of the Mutation Rate of African Cassava Mosaic Virus

2018 ◽  
Vol 2 (1) ◽  
pp. 44-56
Author(s):  
Grey Chibawe ◽  
Lillian Mzyece ◽  
Mayumbo Nyirenda ◽  
Jackson Phiri
Keyword(s):  
Higher Education ◽  
Open Source ◽  
Mosaic Virus ◽  
Life Sciences ◽  
Software Tools ◽  
African Cassava Mosaic Virus ◽  
User Friendly ◽  
Cassava Mosaic Virus ◽  
Analyze Data

Popular tools used in studies in life sciences are often costly. This often pauses challenges to researchers in spite of the fact that research continues to be a key to the successful systematic development of new knowledge and a fundamental aspect to the usefulness of all higher education. Particularly, higher education also aims to advance, create and disseminate knowledge through research. Such critical studies like mutation studies therefore require affordable and fast results yielding software. In such research, open source software tools become handy in place of expensive proprietary tools. In order to provide alternative software tools for research, we decided to use a case study of the mutation of the African Cassava Mosaic Virus (ACMV) done by researchers in Zambia. The study of ACMV mutation is hampered by fragmented and non-user-friendly tools, which are currently available. A number of the tools used also depend on network connection, especially the Internet, to access and analyze data. To help alleviate this problem this research proposes the use of open source libraries in biopython to generate cost efficient and user-friendly solutions. Additionally, we propose the use of an open standard using XML as a standard protocol to share data between applications or stages in genomic data analysis of the ACMV. In our strife to provide open source solutions we analysed various tools and noted that biopython is quite popular. During our study of biopython our initial results show that it’s possible to use free tools to analyze data in the life sciences and consequently reduce the time and cost required to analyze ACMV. Based on this case study we propose the adoption of such open source libraries in order to make research much more affordable for scientists in the life sciences for researches that operate within a constrained budget.

scholarly journals Tribe: The collaborative platform for reproducible web-based analysis of gene sets

2016 ◽  
Author(s):  
René A. Zelaya ◽  
Aaron K. Wong ◽  
Alex T. Frase ◽  
Marylyn D. Ritchie ◽  
Casey S. Greene
Keyword(s):  
Open Source ◽  
Web Interface ◽  
Web Based ◽  
Gene Set ◽  
Collaborative Editing ◽  
Gene Sets ◽  
Collaborative Platform ◽  
Set Up ◽  
User Friendly ◽  
Multi Server

AbstractBackgroundThe adoption of new bioinformatics webservers provides biological researchers with new analytical opportunities but also raises workflow challenges. These challenges include sharing collections of genes with collaborators, translating gene identifiers to the most appropriate nomenclature for each server, tracking these collections across multiple analysis tools and webservers, and maintaining effective records of the genes used in each analysis.DescriptionIn this paper, we present the Tribe webserver (available at https://tribe.greenelab.com), which addresses these challenges in order to make multi-server workflows seamless and reproducible. This allows users to create analysis pipelines that use their own sets of genes in combinations of specialized data mining webservers and tools while seamlessly maintaining gene set version control. Tribe’s web interface facilitates collaborative editing: users can share with collaborators, who can then view, download, and edit these collections. Tribe’s fully-featured API allows users to interact with Tribe programmatically if desired. Tribe implements the OAuth 2.0 standard as well as gene identifier mapping, which facilitates its integration into existing servers. Access to Tribe’s resources is facilitated by an easy-to-install Python application called tribe-client. We provide Tribe and tribe-client under a permissive open-source license to encourage others to download the source code and set up a local instance or to extend its capabilities.ConclusionsThe Tribe webserver addresses challenges that have made reproducible multi-webserver workflows difficult to implement until now. It is open source, has a user-friendly web interface, and provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools.

scholarly journals iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

Megataxa ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
MIGUEL VENCES ◽  
AURÉLIEN MIRALLES ◽  
SOPHIE BROUILLET ◽  
JACQUES DUCASSE ◽  
ALEXANDER FEDOSOV ◽  
...  
Keyword(s):  
Open Source ◽  
User Interfaces ◽  
Species Delimitation ◽  
Statistical Tests ◽  
Future Perspective ◽  
User Friendliness ◽  
Morphometric Analyses ◽  
Data Files ◽  
Set Up ◽  
User Friendly

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org)

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