06/01400 Exergy-based lumped simulation of complex systems: An interactive analysis tool

AbstractBackgroundMultiplex bisulphite PCR sequencing is a convenient and scalable method to comprehensively profile DNA methylation at selected loci. The method is useful for validation of methylation biomarker panels on large clinical cohorts, as it can be applied to DNA isolated from fresh tissue, archival formalin fixed paraffin embedded tissue (FFPET) or circulating cell free DNA in plasma. However, successful clinical implementation of DNA methylation biomarkers for disease detection using multiplex bisulphite PCR sequencing, requires user-friendly sample analysis methods and a diversity of visualisation options, which are not met by current tools.ResultsWe have developed a computational pipeline with an interactive graphical interface, called MethPanel, in order to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. Moreover, MethPanel offers important and unique features, such as calculation of a polymorphism score and bisulphite PCR bias correction capabilities. MethPanel is designed so that the methylation data from all samples can be run in parallel on either a personal computer or a high performance computer. The outputs are also automatically forwarded to a shinyApp for convenient display, visualisation and sharing data with collaborators and clinicians. Importantly the data is centralised in one location, which aids storage management.Availability and ImplementationMethPanel is freely available at https://github.com/thinhong/MethPanelConclusionMethPanel provides a novel parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation marker panels for disease detection.

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KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications

F1000Research ◽

10.12688/f1000research.25523.1 ◽

2020 ◽

Vol 9 ◽

pp. 832

Author(s):

Finn Kuusisto ◽

Daniel Ng ◽

John Steill ◽

Ian Ross ◽

Miron Livny ◽

...

Keyword(s):

Text Mining ◽

Web Application ◽

Biomedical Applications ◽

Analysis Tool ◽

Trial And Error ◽

Web Tool ◽

Interactive Analysis ◽

Term List ◽

Public Resource ◽

The Web

Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at https://www.kinderminer.org.

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Visual Analysis of Sorting and Classification of Multidimensional Data

International Journal of Pattern Recognition and Artificial Intelligence ◽

10.1142/s021800142155003x ◽

2020 ◽

pp. 2155003

Author(s):

Dongsheng Yang ◽

Shidong Yu ◽

Ying Hao

Keyword(s):

Visual Analysis ◽

Visual Display ◽

Complete Classification ◽

Multidimensional Data ◽

Analysis Tool ◽

Interactive Analysis ◽

Attribute Weights ◽

Correlation Structures ◽

Better Than

An important work of data analysis is to identify correlation structures and classify the data in unlabeled high-dimensional data, which usually requires iterative experiments on clustering parameters, attribute weights and instances. For a large dataset, the number of clusters may be huge, and it is a great challenge to explore in this huge space. People usually have a more comprehensive understanding of some data. For example, they think that data A is better than data B, but they do not know which attributes are important. Therefore, a powerful interactive analysis tool can help people greatly improve the effectiveness of exploratory clustering analysis. This paper provides a visual analysis method for sorting and classifying multivariate data. It can determine the weight of each attribute through user’s interaction, thus, generating sorting, and then complete classification according to sorting results. Through visual display, users can understand the characteristics of data as well as category characteristics intuitively and quickly, and it helps users improve sorting and classification results.

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KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications

F1000Research ◽

10.12688/f1000research.25523.2 ◽

2021 ◽

Vol 9 ◽

pp. 832

Author(s):

Finn Kuusisto ◽

Daniel Ng ◽

John Steill ◽

Ian Ross ◽

Miron Livny ◽

...

Keyword(s):

Text Mining ◽

Web Application ◽

Biomedical Applications ◽

Analysis Tool ◽

Trial And Error ◽

Web Tool ◽

Interactive Analysis ◽

Term List ◽

Public Resource ◽

The Web

Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at https://www.kinderminer.org.

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IMPLEMENTATION EFFECTIVENESS OF HOSPITAL RESPONSIBILITY TOWARDS MEDICAL DISPUTE PROCESS AT HOSPITAL X CIBINONG

Jurnal Ilmiah Teunuleh ◽

10.51612/teunuleh.v2i3.59 ◽

2021 ◽

Vol 2 (3) ◽

pp. 15-24

Author(s):

Adelin Litan ◽

Fresley Hutapea ◽

Rina Mutiara

Keyword(s):

Public Relations ◽

Secondary Data ◽

Medical Personnel ◽

Hospital Staff ◽

Analysis Tool ◽

Study Approach ◽

Interactive Analysis ◽

Medical Disputes ◽

Medical Dispute ◽

Laws And Regulations

Medical disputes that are rife in the medical world in Indonesia are a separate burden for medical personnel in carrying out daily practices, where the hospital as a place for medical personnel to work, should be responsible for medical personnel involved in medical disputes. The absence of sufficiently clear regulations governing the responsibility of hospitals in resolving medical disputes, makes medical personnel, in this case, the most disadvantaged part. The purpose of this study is to empirically determine the applicable laws and regulations regarding the responsibility of hospitals in the process of resolving medical disputes and the effectiveness of their implementation. The research method used is qualitative research with case study approach. Data sources are primary and secondary data. The data analysis subjects were informants, namely the director of medical services, the legal department officer and the public relations officer. The analysis tool uses interactive analysis. There were at least 4 laws and regulations related to hospital responsibility for medical personnel and implementation of regulations regarding hospital responsibility towards medical dispute process is 88%. The research found no guidelines for handling medical disputes. This study shows that the laws and regulations related to hospital responsibility and their implementation in the medical dispute resolution process have been implemented. The recommendation to Hospital X Cibinong is to make guidelines on the flow of medical dispute handling and provide education about health law to all hospital staff, especially medical personnel as parties most vulnerable to malpractice suits.

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MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection

Bioinformatics ◽

10.1093/bioinformatics/btaa1060 ◽

2020 ◽

Author(s):

Phuc-Loi Luu ◽

Phuc-Thinh Ong ◽

Tran Thai Huu Loc ◽

Dilys Lam ◽

Ruth Pidsley ◽

...

Keyword(s):

Dna Methylation ◽

Supplementary Information ◽

Complete Analysis ◽

Analysis Tool ◽

Sequencing Data ◽

Interactive Analysis ◽

Disease States ◽

Parallel Pipeline ◽

Analysis Workflow ◽

A Cell

Abstract Summary DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of a epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualisation and remotely sharing data with collaborators and clinicians. Availability MethPanel is freely available at https://github.com/thinhong/MethPanel. Supplementary information Supplementary data are available at Bioinformatics online.

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TAPRAV: An interactive analysis tool for exploring workload aligned to models of task execution

Interacting with Computers ◽

10.1016/j.intcom.2007.01.004 ◽

2007 ◽

Vol 19 (3) ◽

pp. 314-329 ◽

Cited By ~ 5

Author(s):

Brian P. Bailey ◽

Chris W. Busbey ◽

Shamsi T. Iqbal

Keyword(s):

Analysis Tool ◽

Task Execution ◽

Interactive Analysis

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