scholarly journals An open source web application for the surveillance and prevention of the impacts on public health of extreme meteorological events: the SUPREME system

2011 ◽  
Vol 10 (1) ◽  
pp. 39 ◽  
Author(s):  
Steve Toutant ◽  
Pierre Gosselin ◽  
Diane Bélanger ◽  
Ray Bustinza ◽  
Sonia Rivest
2021 ◽  
Author(s):  
Jason Hunter ◽  
Mark Thyer ◽  
Dmitri Kavetski ◽  
David McInerney

<p>Probabilistic predictions provide crucial information regarding the uncertainty of hydrological predictions, which are a key input for risk-based decision-making. However, they are often excluded from hydrological modelling applications because suitable probabilistic error models can be both challenging to construct and interpret, and the quality of results are often reliant on the objective function used to calibrate the hydrological model.</p><p>We present an open-source R-package and an online web application that achieves the following two aims. Firstly, these resources are easy-to-use and accessible, so that users need not have specialised knowledge in probabilistic modelling to apply them. Secondly, the probabilistic error model that we describe provides high-quality probabilistic predictions for a wide range of commonly-used hydrological objective functions, which it is only able to do by including a new innovation that resolves a long-standing issue relating to model assumptions that previously prevented this broad application.  </p><p>We demonstrate our methods by comparing our new probabilistic error model with an existing reference error model in an empirical case study that uses 54 perennial Australian catchments, the hydrological model GR4J, 8 common objective functions and 4 performance metrics (reliability, precision, volumetric bias and errors in the flow duration curve). The existing reference error model introduces additional flow dependencies into the residual error structure when it is used with most of the study objective functions, which in turn leads to poor-quality probabilistic predictions. In contrast, the new probabilistic error model achieves high-quality probabilistic predictions for all objective functions used in this case study.</p><p>The new probabilistic error model and the open-source software and web application aims to facilitate the adoption of probabilistic predictions in the hydrological modelling community, and to improve the quality of predictions and decisions that are made using those predictions. In particular, our methods can be used to achieve high-quality probabilistic predictions from hydrological models that are calibrated with a wide range of common objective functions.</p>


Author(s):  
Morgan Magnin ◽  
Guillaume Moreau ◽  
Nelle Varoquaux ◽  
Benjamin Vialle ◽  
Karen Reid ◽  
...  

A critical component of the learning process lies in the feedback that students receive on their work that validates their progress, identifies flaws in their thinking, and identifies skills that still need to be learned. Many higher-education institutions have developed an active pedagogy that gives students opportunities for different forms of assessment and feedback. This means that students have numerous lab exercises, assignments, and projects. Both instructors and students thus require effective tools to efficiently manage the submission, assessment, and individualized feedback of students’ work. The open-source web application MarkUs aims at meeting these needs: it facilitates the submission and assessment of students’ work. Students directly submit their work using MarkUs, rather than printing it, or sending it by email. The instructors or teaching assistants use MarkUs’s interface to view the students’ work, annotate it, and fill in a marking rubric. Students use the same interface to read the annotations and learn from the assessment. Managing the students’ submissions and the instructors assessments within a single online system, has led to several positive pedagogical outcomes: the number of late submissions has decreased, the assessment time has been drastically reduced, students can access their results and read the instructor’s feedback immediately after the grading process is completed. Using MarkUs has also significantly reduced the time that instructors spend collecting assignments, creating the marking schemes, passing them on to graders, handling special cases, and returning work to the students. In this paper, we introduce MarkUs’ features, and illustrate their benefits for higher education through our own teaching experiences and that of our colleagues. We also describe an important benefit of the fact that the tool itself is open-source. MarkUs has been developed entirely by students giving them a valuable learning opportunity as they work on a large software system that real users depend on. Virtuous circles indeed arise, with former users of MarkUs becoming developers and then supervisors of further development. We will conclude by drawing perspectives about forthcoming features and use, both technically and pedagogically.


2014 ◽  
Vol 102 (1) ◽  
pp. 69-80 ◽  
Author(s):  
Torregrosa Daniel ◽  
Forcada Mikel L. ◽  
Pérez-Ortiz Juan Antonio

Abstract We present a web-based open-source tool for interactive translation prediction (ITP) and describe its underlying architecture. ITP systems assist human translators by making context-based computer-generated suggestions as they type. Most of the ITP systems in literature are strongly coupled with a statistical machine translation system that is conveniently adapted to provide the suggestions. Our system, however, follows a resource-agnostic approach and suggestions are obtained from any unmodified black-box bilingual resource. This paper reviews our ITP method and describes the architecture of Forecat, a web tool, partly based on the recent technology of web components, that eases the use of our ITP approach in any web application requiring this kind of translation assistance. We also evaluate the performance of our method when using an unmodified Moses-based statistical machine translation system as the bilingual resource.


2021 ◽  
Vol 11 (1) ◽  
pp. 1-10
Author(s):  
Toga Aldila Cinderatama ◽  
◽  
Ashafidz Fauzan Dianta ◽  
Fery Sofian Efendi ◽  
Kunti Eliyen ◽  
...  

Tuberculosis (TB) is a chronic disease that is still a public health problem globally, including Indonesia, due to its easy transmission. Treatment for TB sufferers consist of several drug combinations that are intended to eradicate germs. For TB sufferers, the key to successful treatment is the patient's compliance with taking medication every day. The lengthy treatment time is usually at least six months allowing non-adherence to taking the medication by the patient. If not treated properly, there will be a risk of disease complications, such as tuberculosis bacteria resistant to drugs, making TB treatment more difficult. In this study, an Android-based was built to remind TB sufferers to take their medication during the treatment process. In addition to the mobile-based application, there is also a web application used by drug drinking supervisors (PMO; Petugas Minum Obat in Indonesia) in monitoring TB patients, where the application can also view patient compliance statistics in taking medication and historical data on TB patients’ medical treatment. After completion and development, the application will be given to PMO officers and patients to be tested. It is hoped that the application can help the TB treatment process become more effective and prevent treatment failure from the implementation.


2017 ◽  
Author(s):  
James Hadfield ◽  
Colin Megill ◽  
Sidney M. Bell ◽  
John Huddleston ◽  
Barney Potter ◽  
...  

AbstractSummaryUnderstanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike.Availability and implementationAll code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.


2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Edward Daniel ◽  
Goodluck U. Onwukwe ◽  
Rik K. Wierenga ◽  
Susan E. Quaggin ◽  
Seppo J. Vainio ◽  
...  

2021 ◽  
Vol 37 (1) ◽  
pp. 77-84
Author(s):  
Yanbo Huang ◽  
D. K. Fisher

HighlightsA web application for guiding data calculated from distributed weather data through open-source cloud service.A design scheme of portable weather stations built from inexpensive open-source electronics.Integration of open-source hardware and software for online guiding data to avoid drift caused by temperature inversion.Abstract. It is important for agricultural chemical applicators to follow proper spray procedures to prevent susceptible crops, animals, people, or other living organisms from being injured far downwind. Spraying during stable atmospheric conditions should be avoided to prevent surface-temperature inversion-induced off-target drift of crop protection materials. Previous statistical analysis determined times of high likelihood of stable atmospheric conditions, which are unfavorable for spraying, during the day under clear and cloudy conditions in hot summer months in the Mississippi Delta. Results validated the thresholds of temperature increase in the morning and temperature drop in the afternoon with wind speeds and the transition between stable and unstable atmospheric conditions. With this information, an algorithm was developed to calculate if atmospheric conditions were favorable for spraying based on field temperature and wind speed at any instant. With this algorithm, a web application was built to provide real-time determination of atmospheric stability and hourly online recommendation of whether aerial applications were appropriate for a location and time in the Mississippi Delta. This study further developed another web application specifically for Stoneville, Mississippi, with data measured from weather stations constructed from inexpensive open-source electronics, accessories, and software for more accurate online guidance for site-specific drift management. The web application is adapted for accessing on mobile terminals, such as smartphones and tablets, and provides timely guidance for aerial applicators and producers to avoid spray drift and air quality issues long distances downwind in the area. Keywords: Open-source hardware, Open-source software, Spray drift, Temperature inversion, Web application.


2018 ◽  
pp. 175-192
Author(s):  
Peter Costa ◽  
Deborah J. Briggs

Rabies is the deadliest infectious disease known to humans and animals and yet is almost always preventable even after an exposure has occurred. The lack of educational awareness is a major reason why over 55,000 people die of the disease every year. The Global Alliance for Rabies Control, in association with international partners in the field of public health, initiated new educational initiatives aimed at increasing global awareness for those living at daily risk of exposure to rabies. Three of the open source educational initiatives are described in this chapter, including: World Rabies Day; the establishment of a freely accessible scientifically accurate education bank; and hosting global webinars that connect public health experts interested in reducing the burden of rabies in their regions.


Author(s):  
Peter Costa ◽  
Deborah J. Briggs

Rabies is the deadliest infectious disease known to humans and animals and yet is almost always preventable even after an exposure has occurred. The lack of educational awareness is a major reason why over 55,000 people die of the disease every year. The Global Alliance for Rabies Control, in association with international partners in the field of public health, initiated new educational initiatives aimed at increasing global awareness for those living at daily risk of exposure to rabies. Three of the open source educational initiatives are described in this chapter, including: World Rabies Day; the establishment of a freely accessible scientifically accurate education bank; and hosting global webinars that connect public health experts interested in reducing the burden of rabies in their regions.


GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Katrina L Kalantar ◽  
Tiago Carvalho ◽  
Charles F A de Bourcy ◽  
Boris Dimitrov ◽  
Greg Dingle ◽  
...  

Abstract Background Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments. Findings We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. Conclusion The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.


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