scholarly journals Open source tools for geographic analysis in transport planning

2021 ◽  
Author(s):  
Robin Lovelace
Keyword(s):  
User Interface ◽  
Open Source ◽  
Citizen Participation ◽  
Simulation Software ◽  
First Century ◽  
Transport Planning ◽  
Geographic Analysis ◽  
Link Type ◽  
Twenty First Century ◽  
Interactive Map

AbstractGeographic analysis has long supported transport plans that are appropriate to local contexts. Many incumbent ‘tools of the trade’ are proprietary and were developed to support growth in motor traffic, limiting their utility for transport planners who have been tasked with twenty-first century objectives such as enabling citizen participation, reducing pollution, and increasing levels of physical activity by getting more people walking and cycling. Geographic techniques—such as route analysis, network editing, localised impact assessment and interactive map visualisation—have great potential to support modern transport planning priorities. The aim of this paper is to explore emerging open source tools for geographic analysis in transport planning, with reference to the literature and a review of open source tools that are already being used. A key finding is that a growing number of options exist, challenging the current landscape of proprietary tools. These can be classified as command-line interface, graphical user interface or web-based user interface tools and by the framework in which they were implemented, with numerous tools released as R, Python and JavaScript packages, and QGIS plugins. The review found a diverse and rapidly evolving ‘ecosystem’ tools, with 25 tools that were designed for geographic analysis to support transport planning outlined in terms of their popularity and functionality based on online documentation. They ranged in size from single-purpose tools such as the QGIS plugin AwaP to sophisticated stand-alone multi-modal traffic simulation software such as MATSim, SUMO and Veins. Building on their ability to re-use the most effective components from other open source projects, developers of open source transport planning tools can avoid ‘reinventing the wheel’ and focus on innovation, the ‘gamified’ A/B Street https://github.com/dabreegster/abstreet/#abstreet simulation software, based on OpenStreetMap, a case in point. The paper, the source code of which can be found at https://github.com/robinlovelace/open-gat, concludes that, although many of the tools reviewed are still evolving and further research is needed to understand their relative strengths and barriers to uptake, open source tools for geographic analysis in transport planning already hold great potential to help generate the strategic visions of change and evidence that is needed by transport planners in the twenty-first century.

scholarly journals CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation

2020 ◽  
Author(s):  
C.J. Arthurs ◽  
R. Khlebnikov ◽  
A. Melville ◽  
M. Marčan ◽  
A. Gomez ◽  
...  
Keyword(s):  
Open Source ◽  
Mesh Generation ◽  
Simulation Software ◽  
Modelling And Simulation ◽  
Integrated Modelling ◽  
Software Environment ◽  
Element Mesh ◽  
Wide Audience ◽  
Link Type ◽  
Computational Haemodynamics

AbstractIn this work, we describe the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. A key aim of CRIMSON is to create a software environment that makes powerful computational haemodynamics tools accessible to a wide audience, including clinicians and students, both within our research laboratories and throughout the community. The overall philosophy is to leverage best-in-class open source standards for medical image processing, parallel flow computation, geometric solid modelling, data assimilation, and mesh generation. It is actively used by researchers in Europe, North and South America, Asia, and Australia. It has been applied to numerous clinical problems; we illustrate applications of CRIMSON to real-world problems using examples ranging from pre-operative surgical planning to medical device design optimization. CRIMSON binaries for Microsoft Windows 10, documentation and example input files are freely available for download from www.crimson.software, and the source code with compilation instructions is available on GitHub https://github.com/carthurs/CRIMSONFlowsolver (CRIMSON Flowsolver) under the GPL v3.0 license, and https://github.com/carthurs/CRIMSONGUI (CRIMSON GUI), under the AGPL v3.0 license. Support is available on the CRIMSON Google Groups forum, located at https://groups.google.com/forum/#!forum/crimson-users.

scholarly journals Systematic review of descriptions of novel bacterial species: evaluation of the twenty-first century taxonomy through text mining

2020 ◽  
Vol 70 (4) ◽  
pp. 2925-2936
Author(s):  
Fernando Hayashi Sant’Anna ◽  
Keli Cristine Reiter ◽  
Patrícia de Fátima Almeida ◽  
Luciane Maria Pereira Passaglia
Keyword(s):  
Text Mining ◽  
Bacterial Species ◽  
First Century ◽  
Bacterial Taxonomy ◽  
Content Type ◽  
Link Type ◽  
Number Of Species ◽  
Twenty First Century ◽  
The Republic ◽  
Bacterial Characterization

Although described bacterial species increased in the twenty-first century, they correspond to a tiny fraction of the actual number of species living on our planet. The volume of textual data of these descriptions constitutes valuable information for revealing trends that in turn could support strategies for improvement of bacterial taxonomy. In this study, a text mining approach was used to generate bibliometric data to verify the state-of-art of bacterial taxonomy. Around 9700 abstracts of bacterial classification containing the expression ‘sp. nov.’ and published between 2001 and 2018 were downloaded from PubMed and analysed. Most articles were from PR China and the Republic of Korea, and published in the International Journal of Systematic and Evolutionary Microbiology. From about 10 800 species names detected, 93.33 % were considered valid according to the rules of the Bacterial Code, and they corresponded to 82.98 % of the total number of species validated between 2001 and 2018. Streptomyces , Bacillus and Paenibacillus each had more than 200 species described in the period. However, almost 40 % of all species were from the phylum Proteobacteria . Most bacteria were Gram-stain-negative, bacilli and isolated from soil. Thirteen species and one genus homonyms were found. With respect to methodologies of bacterial characterization, the use of terms related to 16S rRNA and polar lipids increased along these years, and terms related to genome metrics only began to appear from 2009 onward, although at a relatively lower frequency. Bacterial taxonomy is known as a conservative discipline, but it gradually changed in terms of players and practices. With the advent of the mandatory use of genomic analyses for species description, we are probably witnessing a turning point in the evolution of bacterial taxonomy.

scholarly journals Integrating geographic analysis in transport planning

2019 ◽  
Author(s):  
Robin Lovelace
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Transport Planning ◽  
Geographic Analysis

Research into and paper about open source software for geographic transport data analysis and planning

scholarly journals MLDSP-GUI: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

2019 ◽  
Author(s):  
Gurjit S. Randhawa ◽  
Kathleen A. Hill ◽  
Lila Kari
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Dna Sequences ◽  
Disease Classification ◽  
Supplementary Information ◽  
Link Type ◽  
Alignment Free ◽  
Comparison And Analysis ◽  
Interactive Graphical User Interface

AbstractSummaryMLDSP-GUI (Machine Learning with Digital Signal Processing) is an open-source, alignment-free, ultrafast, computationally lightweight, standalone software tool with an interactive Graphical User Interface (GUI) for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others.AvailabilityMLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/[email protected] informationSupplementary data are available online.

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