scholarly journals metID: A R package for automatable compound annotation for LC−MS-based data

2021 ◽  
Author(s):  
Xiaotao Shen ◽  
Si Wu ◽  
Liang Liang ◽  
Songjie Chen ◽  
Kevin Contrepois ◽  
...  

Accurate and efficient compound annotation is a long-standing challenge for LC−MSbased data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials.

Author(s):  
Xiaotao Shen ◽  
Si Wu ◽  
Liang Liang ◽  
Songjie Chen ◽  
Kévin Contrepois ◽  
...  

Abstract Summary Accurate and efficient compound annotation is a long-standing challenge for LC−MS-based data (e.g., untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials. Availability and implementation https://jaspershen.github.io/metID. Supplementary information Supplementary data are available at Bioinformatics online.


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>


2018 ◽  
Vol 39 (1) ◽  
pp. 141-146 ◽  
Author(s):  
Fatima Z. Tebbi ◽  
Hadda Dridi ◽  
Mahdi Kalla

AbstractLong term and mid-term reservoir operation involves derivation of rule curves for optimal management of the available resource. The present work deals with reservoir operation in the Aurès arid region. As an example, Babar reservoir is selected to apply the proposed approach which estimates all the water balance terms, especially those which are random as water inflows. For each demand scenario a reservoir operation optimization model using Explicit Stochastic Dynamic Programming (ESDP) is performed, to derive optimal rule curves based on historical operating records (Jan 2002–Dec 2013) and using “Reservoir” R package®. Subsequently, risk analysis is conducted for these different demand scenarios rules by the RRV (reliability, resilience, vulnerability) metrics. Results show the advantage of using the “Reservoir” R package for a rapid and an easy analysis of the performance criteria jointly with the optimization algorithm to Re-operate Reservoir operation.


2019 ◽  
Vol 8 (2) ◽  
pp. 1023-1038

The content of the natural scenes needs to be interpreted which is the primary concern in computer vision. In the advancement of the systems focusing on the intelligent image understanding, the most powerful key is the degree to which meaningful information is extracted by the computer. Moreover with this advancement in the field of image processing, precise and huge information capturing images are desired. The hyperspectral images find its place in such fields of applications. For a single scene, the hyperspectral images (HSI) are composed of hundreds of channels of spectral data. For different materials, with the availability of detailed spectral information, hundreds of contracted bands are collected by hyperspectral sensors. However, with the dimensional complexity, its impact varies from field to field. We reiterate our main focus in this article on providing the various challenges existing relating to HSI and a case study of the current solutions provided for each. A clear depiction of the current issues and approaches in the field of compression as well as some general issues are also discussed towards the end section.


2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Julian Friedrich ◽  
Hans-Peter Hammes ◽  
Guido Krenning

Abstract microRNAs (miRNAs) regulate gene expression and thereby influence biological processes in health and disease. As a consequence, miRNAs are intensely studied and literature on miRNAs has been constantly growing. While this growing body of literature reflects the interest in miRNAs, it generates a challenge to maintain an overview, and the comparison of miRNAs that may function across diverse disease fields is complex due to this large number of relevant publications. To address these challenges, we designed miRetrieve, an R package and web application that provides an overview on miRNAs. By text mining, miRetrieve can characterize and compare miRNAs within specific disease fields and across disease areas. This overview provides focus and facilitates the generation of new hypotheses. Here, we explain how miRetrieve works and how it is used. Furthermore, we demonstrate its applicability in an exemplary case study and discuss its advantages and disadvantages.


2021 ◽  
Author(s):  
Sangeeta Bhatia ◽  
Jack Wardle ◽  
Rebecca K Nash ◽  
Pierre Nouvellet ◽  
Anne Cori

Recent months have demonstrated that emerging variants may set back the global COVID-19 response. The ability to rapidly assess the threat of new variants in real-time is critical for timely optimisation of control strategies. We extend the EpiEstim R package, designed to estimate the time-varying reproduction number (Rt), to estimate in real-time the effective transmission advantage of a new variant compared to a reference variant. Our method can combine information across multiple locations and over time and was validated using an extensive simulation study, designed to mimic a variety of real-time epidemic contexts. We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29, (95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and France respectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) times more transmissible than the wildtype (France data). All results are in line with previous estimates from literature, but could have been obtained earlier and more easily with our off-the-shelf open-source tool. Our tool can be used as an important first step towards quantifying the threat of new variants in real-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor the co-circulation and/or emergence of multiple variants of infectious pathogens.


2020 ◽  
Vol 412 (24) ◽  
pp. 6391-6405 ◽  
Author(s):  
Paula Cuevas-Delgado ◽  
Danuta Dudzik ◽  
Verónica Miguel ◽  
Santiago Lamas ◽  
Coral Barbas

2014 ◽  
Vol 7 (8) ◽  
pp. 2437-2456 ◽  
Author(s):  
T. H. Virtanen ◽  
P. Kolmonen ◽  
E. Rodríguez ◽  
L. Sogacheva ◽  
A.-M. Sundström ◽  
...  

Abstract. An algorithm is presented for the estimation of volcanic ash plume top height using the stereo view of the Advanced Along Track Scanning Radiometer (AATSR) aboard Envisat. The algorithm is based on matching top of the atmosphere (TOA) reflectances and brightness temperatures of the nadir and 55° forward views, and using the resulting parallax to obtain the height estimate. Various retrieval parameters are discussed in detail, several quality parameters are introduced, and post-processing methods for screening out unreliable data have been developed. The method is compared to other satellite observations and in situ data. The proposed algorithm is designed to be fully automatic and can be implemented in operational retrieval algorithms. Combined with automated ash detection using the brightness temperature difference between the 11 and 12 μm channels, the algorithm allows efficient simultaneous retrieval of the horizontal and vertical dispersion of volcanic ash. A case study on the eruption of the Icelandic volcano Eyjafjallajökull in 2010 is presented.


RSC Advances ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 3459-3471 ◽  
Author(s):  
Ananda da Silva Antonio ◽  
Ana Tayná Chaves Aguiar ◽  
Gustavo Ramalho Cardoso dos Santos ◽  
Henrique Marcelo Gualberto Pereira ◽  
Valdir Florêncio da Veiga-Junior ◽  
...  

Several extraction parameters were evaluated in order to establish their influence on the chemosystematic research of angiosperms.


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