DropMS: Petroleomics Data Treatment Based in Web Server for High-Resolution Mass Spectrometry

Rosa, Thalles Ramon; Folli, Gabrielly S.; Pacheco, Wagner Ls; Castro, Marcela Paola; Romão, Wanderson; Filgueiras, Paulo R.

doi:10.1021/jasms.0c00109

Cited by 13 publications

(7 citation statements)

References 30 publications

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“…Considering the development status and theoretical basis of ITS, the system is based on cognitive science theory, adopts the "double master" teaching mode, combines agent technology with ITS, adds a multiagent layer in the middle of the traditional B/S structure system, and forms a three-tier structure model of B/MA/S, namely, Browser/Multiagent Server [36]. Dynamically adjust the teaching strategy according to the specific situation in the teaching process, so as to realize intelligent teaching.…”

Section: Higher Education System Designmentioning

confidence: 99%

Design of Higher Education System Based on Artificial Intelligence Technology

Li¹,

Yang

et al. 2021

Discrete Dynamics in Nature and Society

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In order to solve the problems of low security and response efficiency and slow running speed of the current designed higher education system, a higher education system based on artificial intelligence technology is designed. Firstly, according to the characteristics of artificial intelligence technology, intelligent teaching system, agent technology, and data mining technology are introduced in detail. Then it analyzes the overall and detailed functional requirements of the system and adaptively generates knowledge content and teaching mode suitable for students’ ability and personality by using intelligent reasoning ability and the collection and analysis of students’ personality characteristics. Through data mining of intelligent teaching system, the decision tree about curriculum is obtained, and the students’ cognitive ability is calculated. Based on the theory of cognitive science, using the “double master” teaching mode, combined with agent technology and intelligent teaching system, the system function is divided into six modules. Through the design of database structure and data table, the design of higher education system based on artificial intelligence technology is realized. The experimental results show that the proposed method has high security and response efficiency, fast running speed, and good teaching effect.

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Section: Higher Education System Designmentioning

confidence: 99%

Design of Higher Education System Based on Artificial Intelligence Technology

Li¹,

Yang

et al. 2021

Discrete Dynamics in Nature and Society

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“…DropMS, is a online tool with a user-friendly and browser-based interface to facilitate the processing of high resolution and precision oil mass spectrometry data for petroleomics applications (Rosa et al 2020 ). Uploaded mass spectra to the server are processed using various algorithms reported in the literature, such as S/N ratio filters, recalibrations, chemical formula assimilations and data visualization using graphs and diagrams popularly known in mass spectrometry such as Van Krevelen and Kendrick diagrams among other visualizations.…”

Section: Multifunctional Toolsmentioning

confidence: 99%

New software tools, databases, and resources in metabolomics: updates from 2020

Misra

2021

Metabolomics

151

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Background Precision medicine, space exploration, drug discovery to characterization of dark chemical space of habitats and organisms, metabolomics takes a centre stage in providing answers to diverse biological, biomedical, and environmental questions. With technological advances in mass-spectrometry and spectroscopy platforms that aid in generation of information rich datasets that are complex big-data, data analytics tend to co-evolve to match the pace of analytical instrumentation. Software tools, resources, databases, and solutions help in harnessing the concealed information in the generated data for eventual translational success. Aim of the review In this review, ~ 85 metabolomics software resources, packages, tools, databases, and other utilities that appeared in 2020 are introduced to the research community. Key scientific concepts of review In Table 1 the computational dependencies and downloadable links of the tools are provided, and the resources are categorized based on their utility. The review aims to keep the community of metabolomics researchers updated with all the resources developed in 2020 at a collated avenue, in line with efforts form 2015 onwards to help them find these at one place for further referencing and use.

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“…MetaboAnalyst [29], and DropMS [30]. Even though the graphic user interface (GUI) of these software packages is user friendly, these types of software can be very restrictive in their use and do not allow users to fully customize their analysis to their research needs.…”

Section: Most Recently Coremsmentioning

confidence: 99%

“…These large datasets often require specialized data analysis pipelines for filtering, interrogation, comparison, and visualization [26]. Open-source software and pipelines available for the analysis and visualization of FTICR-MS data include web-based applications such as UltraMassExplorer (UME) [27], FREDA [28], MetaboAnalyst [29], and DropMS [30]. Even though the graphic user interface (GUI) of these software packages is user friendly, these types of software can be very restrictive in their use and do not allow users to fully customize their analysis to their research needs.…”

Section: Introductionmentioning

confidence: 99%

MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data

Ayala-Ortiz

Graf-Grachet

Freire-Zapata

et al. 2022

Preprint

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Background: Microbiomes are now recognized as main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e. metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line based pipeline for the analysis, visualization, and presentation of metabolomics data by direct injection FTICR-MS after molecular formula assignment has been performed. When compared to all other available FTICR software, MetaboDirect is superior with respect to its compute time as it only requires a single line of code that launches a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences that provide a comprehensive experimental assessment of metabolite connectives within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of the microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FTICR-MS-based metabolomics datasets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the FTICR-MS research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. Source code and User guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/) respectively.

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DropMS: Petroleomics Data Treatment Based in Web Server for High-Resolution Mass Spectrometry

Cited by 13 publications

References 30 publications

Design of Higher Education System Based on Artificial Intelligence Technology

Design of Higher Education System Based on Artificial Intelligence Technology

New software tools, databases, and resources in metabolomics: updates from 2020

MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data

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