scholarly journals Transit Analysis Package: An IDL Graphical User Interface for Exoplanet Transit Photometry

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
J. Zachary Gazak ◽  
John A. Johnson ◽  
John Tonry ◽  
Diana Dragomir ◽  
Jason Eastman ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Likelihood Function ◽  
Light Curves ◽  
Parameter Uncertainties ◽  
Data Set ◽  
Specific Data ◽  
Software Release ◽  
Analysis Package ◽  
Good Agreement

We present an IDL graphical user-interface-driven software package designed for the analysis of exoplanet transit light curves. The Transit Analysis Package (TAP) software uses Markov Chain Monte Carlo (MCMC) techniques to fit light curves using the analytic model of Mandal and Agol (2002). The package incorporates a wavelet-based likelihood function developed by Carter and Winn (2009), which allows the MCMC to assess parameter uncertainties more robustly than classicχ2methods by parameterizing uncorrelated “white” and correlated “red” noise. The software is able to simultaneously analyze multiple transits observed in different conditions (instrument, filter, weather, etc.). The graphical interface allows for the simple execution and interpretation of Bayesian MCMC analysis tailored to a user’s specific data set and has been thoroughly tested on ground-based andKeplerphotometry. This paper describes the software release and provides applications to new and existing data. Reanalysis of ground-based observations of TrES-1b, WASP-4b, and WASP-10b (Winn et al., 2007, 2009; Johnson et al., 2009; resp.) and space-basedKepler4b–8b (Kipping and Bakos 2010) show good agreement between TAP and those publications. We also present new multi-filter light curves of WASP-10b and we find excellent agreement with previously published values for a smaller radius.

scholarly journals Highly Automated Dipole EStimation (HADES)

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
C. Campi ◽  
A. Pascarella ◽  
A. Sorrentino ◽  
M. Piana
Keyword(s):  
Inverse Problem ◽  
User Interface ◽  
Graphical User Interface ◽  
Particle Filtering ◽  
Synthetic Data ◽  
Nonlinear Relationship ◽  
Data Set ◽  
Automatic Estimation ◽  
Dipole Estimation ◽  
Dipolar Model

Automatic estimation of current dipoles from biomagnetic data is still a problematic task. This is due not only to the ill-posedness of the inverse problem but also to two intrinsic difficulties introduced by the dipolar model: the unknown number of sources and the nonlinear relationship between the source locations and the data. Recently, we have developed a new Bayesian approach, particle filtering, based on dynamical tracking of the dipole constellation. Contrary to many dipole-based methods, particle filtering does not assume stationarity of the source configuration: the number of dipoles and their positions are estimated and updated dynamically during the course of the MEG sequence. We have now developed a Matlab-based graphical user interface, which allows nonexpert users to do automatic dipole estimation from MEG data with particle filtering. In the present paper, we describe the main features of the software and show the analysis of both a synthetic data set and an experimental dataset.

scholarly journals Advanced Presentation of BETHSY 6.2TC Test Results Calculated by RELAP5 and TRACE

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Andrej Prošek ◽  
Ovidiu-Adrian Berar
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Computer Code ◽  
Nuclear Regulatory Commission ◽  
Equivalent Diameter ◽  
Test Results ◽  
Software Applications ◽  
Analysis Package ◽  
Regulatory Commission ◽  
Physical Phenomena

Today most software applications come with a graphical user interface, including U.S. Nuclear Regulatory Commission TRAC/RELAP Advanced Computational Engine (TRACE) best-estimate reactor system code. The graphical user interface is called Symbolic Nuclear Analysis Package (SNAP). The purpose of the present study was to assess the TRACE computer code and to assess the SNAP capabilities for input deck preparation and advanced presentation of the results. BETHSY 6.2 TC test was selected, which is 15.24 cm equivalent diameter horizontal cold leg break. For calculations the TRACE V5.0 Patch 1 and RELAP5/MOD3.3 Patch 4 were used. The RELAP5 legacy input deck was converted to TRACE input deck using SNAP. The RELAP5 and TRACE comparison to experimental data showed that TRACE results are as good as or better than the RELAP5 calculated results. The developed animation masks were of great help in comparison of results and investigating the calculated physical phenomena and processes.

scholarly journals HTML FORM GENERATOR BASED ON TABLE USING OBJECT ORIENTED PROGRAMMING

2019 ◽  
Vol 3 (1) ◽  
pp. 11-20
Author(s):  
Katon Wijana
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Object Oriented ◽  
Object Oriented Programming ◽  
Data Type ◽  
Web Based ◽  
Specific Data ◽  
Type Size ◽  
User Intervention ◽  
Attribute Type

To insert new data into a database table using a web-based application, a graphical user interface in the form of HTML Form is required. Each table field / attribute requires an appropriate form control in order to minimize data errors that will be entered. There is a relation between the data type of a field in the table with the type of form control to be used, therefore the graphical user interface in the form of HTML Form can be created automatically.  There are various control forms of HTML in the form of tags, generally in the form of input tags. What distinguishes the form control from one to another is the attribute: type, size, value therefore to determine the type and content of form controls can be given through parameters.  HTML Form can be regarded as an object which has many other objects in the form of form controls. Object Oriented Programming (OOP) paradigm it can be implemented to build HTML Form.  Through meta data from a table, it will be able to obtain the appropriate HTML form control, but for each specific data type it can have the appropriate form control candidate, therefore before Form HTML is created by the generator, there should be a little user intervention to get the interface The desired HTML form.

scholarly journals TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

2021 ◽  
Vol 4 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Arne Beermann ◽  
Florian Leese
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Distribution Patterns ◽  
Assessment Tools ◽  
Biological Information ◽  
Distribution Data ◽  
Global Biodiversity Information Facility ◽  
Data Set ◽  
Wide Range ◽  
Dna Metabarcoding

DNA-based identification methods, such as DNA metabarcoding, are increasingly used as biodiversity assessment tools in research and environmental management. Although powerful analysis software exists to process raw data, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the need for easy-to-use, graphical user interface (GUI) software to analyze and visualize DNA metabarcoding data is growing. Here we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualization workflows. The input format of TTT is a so-called "TaXon table". This data format can easily be generated within TTT from two common file formats that can be obtained using various published DNA metabarcoding pipelines: a read table and a taxonomy table. TTT offers a wide range of processing, filtering and analysis modules. The user can analyze and visualize basic statistics, such as read proportion per taxon, as well as more sophisticated visualizations such as interactive Krona charts for taxonomic data exploration, or complex parallel category diagrams to assess species distribution patterns. Venn diagrams can be calculated to compare taxon overlap among replicates, samples, or analysis methods. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, rarefaction analyses, and principal coordinate or non-metric multidimensional scaling plots. The taxonomy of a data set can be validated via the Global Biodiversity Information Facility (GBIF) API to check for synonyms and spelling mistakes. Furthermore, geographical distribution data can be automatically downloaded from GBIF. Additionally, TTT offers a conversion tool for DNA metabarcoding data into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. Beyond that, TTT is able to produce fully interactive html-based graphics that can be analyzed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).

scholarly journals CEPS: An Open Access MATLAB Graphical User Interface (GUI) for the Analysis of Complexity and Entropy in Physiological Signals

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 321
Author(s):  
David Mayor ◽  
Deepak Panday ◽  
Hari Kala Kandel ◽  
Tony Steffert ◽  
Duncan Banks
Keyword(s):  
User Interface ◽  
Open Access ◽  
Graphical User Interface ◽  
Linear Time ◽  
Physiological Signals ◽  
Physiological Data ◽  
Data Set ◽  
Convenience Sample ◽  
Paced Breathing ◽  
Entropy Measures

Background: We developed CEPS as an open access MATLAB® GUI (graphical user interface) for the analysis of Complexity and Entropy in Physiological Signals (CEPS), and demonstrate its use with an example data set that shows the effects of paced breathing (PB) on variability of heart, pulse and respiration rates. CEPS is also sufficiently adaptable to be used for other time series physiological data such as EEG (electroencephalography), postural sway or temperature measurements. Methods: Data were collected from a convenience sample of nine healthy adults in a pilot for a larger study investigating the effects on vagal tone of breathing paced at various different rates, part of a development programme for a home training stress reduction system. Results: The current version of CEPS focuses on those complexity and entropy measures that appear most frequently in the literature, together with some recently introduced entropy measures which may have advantages over those that are more established. Ten methods of estimating data complexity are currently included, and some 28 entropy measures. The GUI also includes a section for data pre-processing and standard ancillary methods to enable parameter estimation of embedding dimension m and time delay τ (‘tau’) where required. The software is freely available under version 3 of the GNU Lesser General Public License (LGPLv3) for non-commercial users. CEPS can be downloaded at https://bitbucket.org/deepak_panday/ceps/src/pipeline_v2/. In our illustration on PB, most complexity and entropy measures decreased significantly in response to breathing at 7 breaths per minute, differentiating more clearly than conventional linear, time- and frequency-domain measures between breathing states. In contrast, Higuchi fractal dimension increased during paced breathing. Conclusions: We have developed CEPS software as a physiological data visualiser able to integrate state of the art techniques. The interface is designed for clinical research and has a structure designed for integrating new tools. The aim is to strengthen collaboration between clinicians and the biomedical community, as demonstrated here by using CEPS to analyse various physiological responses to paced breathing.

EnGenIUS — ENVIRONMENTAL GENOME INFORMATIONAL UTILITY SYSTEM

2008 ◽  
Vol 06 (06) ◽  
pp. 1193-1211 ◽  
Author(s):  
MIHAILO KAPLAREVIC ◽  
ALISON E. MURRAY ◽  
STEPHEN C. CARY ◽  
GUANG R. GAO
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Relational Databases ◽  
Gene Encoding ◽  
Data Set ◽  
Annotation Pipeline ◽  
Genomic Libraries ◽  
Genome Data ◽  
Utility System ◽  
Environmental Genome

Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (> 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset.

scholarly journals HTML FORM GENERATOR BASED ON TABLE USING OBJECT ORIENTED PROGRAMMING

2019 ◽  
Vol 3 (1) ◽  
pp. 11-20
Author(s):  
Katon Wijana
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Object Oriented ◽  
Object Oriented Programming ◽  
Data Type ◽  
Web Based ◽  
Specific Data ◽  
Type Size ◽  
User Intervention ◽  
Attribute Type

To insert new data into a database table using a web-based application, a graphical user interface in the form of HTML Form is required. Each table field / attribute requires an appropriate form control in order to minimize data errors that will be entered. There is a relation between the data type of a field in the table with the type of form control to be used, therefore the graphical user interface in the form of HTML Form can be created automatically.  There are various control forms of HTML in the form of tags, generally in the form of input tags. What distinguishes the form control from one to another is the attribute: type, size, value therefore to determine the type and content of form controls can be given through parameters.  HTML Form can be regarded as an object which has many other objects in the form of form controls. Object Oriented Programming (OOP) paradigm it can be implemented to build HTML Form.  Through meta data from a table, it will be able to obtain the appropriate HTML form control, but for each specific data type it can have the appropriate form control candidate, therefore before Form HTML is created by the generator, there should be a little user intervention to get the interface The desired HTML form.

XDSAPP: a graphical user interface for the convenient processing of diffraction data usingXDS

2012 ◽  
Vol 45 (3) ◽  
pp. 568-572 ◽  
Author(s):  
Michael Krug ◽  
Manfred S. Weiss ◽  
Udo Heinemann ◽  
Uwe Mueller
Keyword(s):  
User Interface ◽  
Data Collection ◽  
Data Processing ◽  
Graphical User Interface ◽  
Diffraction Data ◽  
Easy Access ◽  
Translational Symmetry ◽  
Data Sets ◽  
Data Set ◽  
Radiation Decay

XDSAPPis a Tcl/Tk-based graphical user interface for the easy and convenient processing of diffraction data sets usingXDS. It provides easy access to allXDSfunctionalities, automates the data processing and generates graphical plots of various data set statistics provided byXDS. By incorporating additional software, further information on certain features of the data set, such as radiation decay during data collection or the presence of pseudo-translational symmetry and/or twinning, can be obtained. Intensity files suitable forCCP4,CNSandSHELXare generated.

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