scholarly journals Towards the Development of Language Analysis Tools for the Written Latgalian Language

2020 ◽  
Author(s):  
Daiga Deksne ◽  
Anna Vulāne
Keyword(s):  
Web Service ◽  
Morphological Analysis ◽  
Written Language ◽  
Analysis Tool ◽  
Tool Development ◽  
Joint Effort ◽  
Analysis Tools ◽  
Language Analysis ◽  
Wide Range ◽  
Development Of Language

This paper reports on the development of spell checking and morphological analysis tools for Latgalian. The Latgalian written language is a historic variant of the Latvian language. There is a wide range of language analysis tools available for Latvian, whereas the Latgalian language lacks such tools. The work is done by the joint effort of linguists who work on morphologically marked lexicon creation and IT specialists who work on language tool development. For the creation of a morphological analysis tool, we reuse the FST technology used for the Latvian morphological analyzer. We create a spelling dictionary that can be used with the Hunspell engine. All tools are accessible via Web Service. For now, the Latgalian lexicon contains 13,139 lemmas marked by 105 inflection groups. The work of lexicon replenishment still continues.

A New Analysis Tool for Continuous Glucose Monitor Data

2021 ◽  
pp. 193229682110289
Author(s):  
Evan Olawsky ◽  
Yuan Zhang ◽  
Lynn E Eberly ◽  
Erika S Helgeson ◽  
Lisa S Chow
Keyword(s):  
Glucose Monitoring ◽  
Glycemic Variability ◽  
R Package ◽  
Analysis Tool ◽  
Continuous Glucose Monitor ◽  
Analysis Tools ◽  
R Shiny ◽  
Primary Driver ◽  
Rich Information ◽  
Web App

Background: With the development of continuous glucose monitoring systems (CGMS), detailed glycemic data are now available for analysis. Yet analysis of this data-rich information can be formidable. The power of CGMS-derived data lies in its characterization of glycemic variability. In contrast, many standard glycemic measures like hemoglobin A1c (HbA1c) and self-monitored blood glucose inadequately describe glycemic variability and run the risk of bias toward overreporting hyperglycemia. Methods that adjust for this bias are often overlooked in clinical research due to difficulty of computation and lack of accessible analysis tools. Methods: In response, we have developed a new R package rGV, which calculates a suite of 16 glycemic variability metrics when provided a single individual’s CGM data. rGV is versatile and robust; it is capable of handling data of many formats from many sensor types. We also created a companion R Shiny web app that provides these glycemic variability analysis tools without prior knowledge of R coding. We analyzed the statistical reliability of all the glycemic variability metrics included in rGV and illustrate the clinical utility of rGV by analyzing CGM data from three studies. Results: In subjects without diabetes, greater glycemic variability was associated with higher HbA1c values. In patients with type 2 diabetes mellitus (T2DM), we found that high glucose is the primary driver of glycemic variability. In patients with type 1 diabetes (T1DM), we found that naltrexone use may potentially reduce glycemic variability. Conclusions: We present a new R package and accompanying web app to facilitate quick and easy computation of a suite of glycemic variability metrics.

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

Modeling framework for IoT integration of building automation systems

2017 ◽  
Vol 65 (9) ◽  
Author(s):  
Daniel Schachinger ◽  
Andreas Fernbach ◽  
Wolfgang Kastner
Keyword(s):  
Web Services ◽  
Web Service ◽  
Building Automation ◽  
Modeling Framework ◽  
Seamless Integration ◽  
Automation Systems ◽  
Wide Range ◽  
Machine To Machine Communication ◽  
Machine Communication ◽  
The Internet Of Things

AbstractAdvancements within the Internet of Things are leading to a pervasive integration of different domains including also building automation systems. As a result, device functionality becomes available to a wide range of applications and users outside of the building automation domain. In this context, Web services are identified as suitable solution for machine-to-machine communication. However, a major requirement to provide necessary interoperability is the consideration of underlying semantics. Thus, this work presents a universal framework for tag-based semantic modeling and seamless integration of building automation systems via Web service-based technologies. Using the example of the KNX Web services specification, the applicability of this approach is pointed out.

scholarly journals StrainPro – a highly accurate Metagenomic strain-level profiling tool

2019 ◽  
Author(s):  
Hsin-Nan Lin ◽  
Yaw-Ling Lin ◽  
Wen-Lian Hsu
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Taxonomic Diversity ◽  
Evaluation Study ◽  
Taxonomic Composition ◽  
Strain Level ◽  
Metagenomic Analysis ◽  
Reference Database ◽  
Analysis Tool ◽  
Analysis Tools

ABSTRACTCharacterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA fragment sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. However, only a few tools could achieve strain-level identification and most tools estimate the microbial abundances simply according to the read counts. An evaluation study on metagenomic analysis tools concludes that the predicted abundance differed significantly from the true abundance. In this study, we present StrainPro, a novel metagenomic analysis tool which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences. We compare the performance of StrainPro with seven existing tools. The results show that StrainPro not only identifies metagenomes with high precision and recall, but it is also highly robust even when the metagenomes are not included in the reference database. Moreover, StrainPro estimates the relative abundance with high accuracy. We demonstrate that there is a strong positive linear relationship between observed and predicted abundances.

scholarly journals Advanced Cluster and Predictive Analysis Tool Development for Commercial Office Real Estate Energy Usage

2021 ◽  
Author(s):  
Carleen Lawson
Keyword(s):  
Energy Use ◽  
Data Gathering ◽  
Machine Learning Algorithms ◽  
Analysis Tool ◽  
Tool Development ◽  
Energy Usage ◽  
Future Data ◽  
Building Characteristics ◽  
Energy Benchmarking ◽  
Physical Features

From 2009-2015, REALPAC collected monthly energy usage and building characteristics for over 500 buildings in the 20 by ‘15 Energy Benchmarking Survey (REALPAC, 2009). While preliminary analysis had been completed on this dataset, this research undertook an in-depth statistical analysis of the data to identify trends and important variables. Eight machine learning algorithms were employed to predict energy usage as a function of previous energy use and select physical features. The dataset did not possess the appropriate variables to predict such usage accurately. Characteristics such as building system efficiency, construction assemblies, condition, compactness, and window to wall ratio are thus recommended for inclusion in future data-gathering initiatives. https://digital.library.ryerson.ca/islandora/object/RULA:8631/datastream/LAW_RSCR-4.80MB/view https://digital.library.ryerson.ca/islandora/object/RULA:8631/datastream/LAW-ExTa-428KB/view https://digital.library.ryerson.ca/islandora/object/RULA:8631/datastream/LAW-ExGa-5.62MB/view https://digital.library.ryerson.ca/islandora/object/RULA:8631/datastream/LAW-DATA-1.9MB/view

scholarly journals IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites

mBio ◽  
2015 ◽  
Vol 6 (4) ◽  
Author(s):  
Michalis Hadjithomas ◽  
I-Min Amy Chen ◽  
Ken Chu ◽  
Anna Ratner ◽  
Krishna Palaniappan ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolism ◽  
Genomic Data ◽  
Gene Clusters ◽  
Metagenomic Data ◽  
Integrated Analysis ◽  
Analysis Tool ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Analysis Tools

ABSTRACTIn the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of “big” genomic data for discovering small molecules. IMG-ABC relies on IMG's comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC's focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time inAlphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules.IMPORTANCEIMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG's extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world.

Semantic Web Service Discovery

2011 ◽  
pp. 240-280 ◽  
Author(s):  
V. Tsetsos
Keyword(s):  
Semantic Web ◽  
Web Service ◽  
Service Discovery ◽  
Semantic Web Service ◽  
Web Service Discovery ◽  
Wide Range ◽  
Near Future ◽  
Semantic Web Service Discovery ◽  
Current Systems ◽  
Semantic Discovery

This chapter surveys existing approaches to Semantic Web service discovery. Such semantic discovery will probably substitute existing keyword-based solutions in the near future, in order to overcome the limitations of the latter. First, the architectural components along with potential deployment scenarios are discussed. Subsequently, a wide range of algorithms and tools that have been proposed for the realization of Semantic Web service discovery are presented. Moreover, key challenges and open issues, not addressed by current systems, are identified. The purpose of this chapter is to update the reader on the current progress in this area of the distributed systems domain and to provide the required background knowledge and stimuli for further research and experimentation in semantics-based service discovery.

scholarly journals Studying State Convergence of Input-to-State Stable Systems with Applications to Power System Analysis

Energies ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 92 ◽  
Author(s):  
Antonio T. Alexandridis
Keyword(s):  
Nonlinear Systems ◽  
Power Systems ◽  
Power System ◽  
System Analysis ◽  
Nonlinear Models ◽  
Sufficient Conditions ◽  
Stability And Convergence ◽  
Convergence To Equilibrium ◽  
Analysis Tool ◽  
Wide Range

In stability studies, the response of a system enforced by external, known or unknown, inputs is of great importance. Although such an analysis is quite easy for linear systems, it becomes a cumbersome task when nonlinearities exist in the system model. Nevertheless, most of the real-world systems are externally enforced nonlinear systems with nonzero equilibriums. Representative examples in this category include power systems, where studies on stability and convergence to equilibrium constitute crucial objectives. Driven by this need, the aim of the present work is twofold: First, to substantially complete the theoretical infrastructure by establishing globally valid sufficient conditions for externally enforced nonlinear systems that converge to nonzero equilibriums and, second, to deploy an efficient method easily applicable on practical problems as it is analyzed in detail on a typical power system example. To that end, in the theoretical first part of the paper, a rigorous nonlinear analysis is developed. Particularly, starting from the well-established nonlinear systems theory based on Lyapunov techniques and on the input-to-state stability (ISS) notion, it is proven after a systematic and lengthy analysis that ISS can also guarantee convergence to nonzero equilibrium. Two theorems and two corollaries are established to provide the sufficient conditions. As shown in the paper, the main stability and convergence objectives for externally enforced systems are fulfilled if simple exponential or asymptotic converging conditions can be proven for the unforced system. Then, global or local convergence is established, respectively, while for the latter case, a novel method based on a distance-like measure for determining the region of attraction (RoA) is proposed. The theoretical results are examined on classic power system generation nonlinear models. The power system examples are suitably selected in order to effectively demonstrate the proposed method as a stability analysis tool and to validate all the particular steps, especially that of evaluating the RoA. The examined system results clearly verify the theoretical part, indicating a rather wide range of applications in power systems.

DP-Stability During Heavy Lift Operations Using a Modified Kalman Filter

2018 ◽  
Author(s):  
Eelco Harmsen ◽  
Radboud van Dijk ◽  
Petter Stuberg
Keyword(s):  
Kalman Filter ◽  
Dynamic Positioning ◽  
Mooring System ◽  
Engineering Analysis ◽  
Single Object ◽  
Joint Effort ◽  
Wide Range ◽  
Floating Object ◽  
Heavy Lift ◽  
Modified Kalman Filter

During heavy lift operations, staying on position using a Dynamic Positioning (DP) system offers many advantages compared with a mooring system. However, when the vessel is connected to another fixed or floating object during the lifting operation through its hoist wires it may experience instabilities in the DP-system. These DP-instabilities are caused by the inability of the DP system to handle the relatively stiff external spring of the hoist wire correctly. This phenomenon is well known and mitigating measures such as Heavy Lift Mode have been developed over the years that work well for stationary vessels. However, when two vessels are lifting a single object together (e.g. QUAD lift), existing solutions to prevent this DP-instability are insufficient, as the nature of such lift requires a synchronous move on DP. During studies to the fundamental behavior of a DP system during heavy lift operations it is found that modifications to the Kalman filter can prevent these DP-instabilities. Heerema Marine Contractors presented the DP-stability challenges to Kongsberg Maritime, and a joint effort resulted in an implementation of a modified Kalman filter in the Kongsberg Maritime DP system. Also a dedicated engineering analysis to predict risk of DP-instabilities for specific lift configurations has been developed. The modified DP-system is tested in large number of simulations (both desktop and a full mission simulator) to test the ability of the updated DP-system to deal with a wide range of specific heavy lift conditions. Results were evaluated between Heerema office, Kongsberg and offshore personnel for developing the optimum Kalman filter parameters. Finally, the system is tested during a dedicated DP-trial program onboard Thialf. As the results of all these tests were very successful, the new High Kalman filter was made available onboard Thialf as a permanent option next to the original functionalities. The paper addresses the steps followed to define the new Kalman filter settings, the simulations performed to test the new filter as well as to show results of the offshore tests that were done to validate the numerical analysis.

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