scholarly journals A new method for inferring timetrees from temporally sampled molecular sequences

2019 ◽  
Author(s):  
Sayaka Miura ◽  
Koichiro Tamura ◽  
Sergei L. Kosakovsky Pond ◽  
Louise A. Huuki ◽  
Jessica Priest ◽  
...  
Keyword(s):  
User Interface ◽  
High Throughput ◽  
Graphical User Interface ◽  
Bayesian Methods ◽  
New Method ◽  
Divergence Times ◽  
Bayesian Approaches ◽  
History Of ◽  
Cross Platform ◽  
Better Than

ABSTRACTPathogen timetrees are phylogenies scaled to time. They reveal the temporal history of a pathogen spread through the populations as captured in the evolutionary history of strains. These timetrees are inferred by using molecular sequences of pathogenic strains sampled at different times. That is, temporally sampled sequences enable the inference of sequence divergence times. Here, we present a new approach (RelTime with Dated Tips [RTDT]) to estimating pathogen timetrees based on the relative rate framework underlying the RelTime approach. RTDT does not require many of the priors demanded by Bayesian approaches, and it has light computing requirements. We found RTDT to be accurate on simulated datasets evolved under a variety of branch rates models. Interestingly, we found two non-Bayesian methods (RTDT and Least Squares Dating [LSD]) to perform similar to or better than the Bayesian approaches available in BEAST and MCMCTree programs. RTDT method was found to generally outperform all other methods for phylogenies in with autocorrelated evolutionary rates. In analyses of empirical datasets, RTDT produced dates that were similar to those from Bayesian analyses. Speed and accuracy of the new method, as compared to the alternatives, makes it appealing for analyzing growing datasets of pathogenic strains. Cross-platform MEGA X software, freely available from http://www.megasoftware.net, now contains the new method for use through a friendly graphical user interface and in high-throughput settings.AUTHOR SUMMARYPathogen timetrees trace the origins and evolutionary histories of strains in populations, hosts, and outbreaks. The tips of these molecular phylogenies often contain sampling time information because the sequences were generally obtained at different times during the disease outbreaks and propagation. We have developed a new method for inferring timetrees for phylogenies with tip dates, which improves on widely-used Bayesian methods (e.g., BEAST) in computational efficiency and does not require prior specification of population parameters, branch rate model, or clock model. We performed extensive computer simulation and found that RTDT performed better than the other methods for the estimation of divergence times at deep node in phylogenies where evolutionary rates were autocorrelated. The new method is available in the cross-platform MEGA software package that provides a graphical user interface, and allows use via a command line in scripting and high throughput analysis (www.megasoftware.net).

A New Paradigm for Ship Design Calculations

2015 ◽  
Author(s):  
Stephen M. Hollister
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Ship Design ◽  
New Paradigm ◽  
New Model ◽  
Analysis Tools ◽  
Cross Platform ◽  
Open Code ◽  
Design Calculations ◽  
Interactive Graphical User Interface

A new model for ship design calculations is presented that separates the graphical user interface (GUI) from the calculations (CALC). Design programs can now be defined as more than one interactive graphical user interface tied to one calculation. Several different GUIs can be created for one CALC engine and one GUI can be created to launch several CALC engines in sequence. The GUI of choice is a spreadsheet due to its availability, programmable customization, powerful analysis tools, cross-platform capability, and open code environment.

GEView (Gene Expression View) Tool for Intuitive and High Accessible Visualization of Expression Data for Non-Programmer Biologists

2020 ◽  
pp. 580-592
Author(s):  
Libi Hertzberg ◽  
Assif Yitzhaky ◽  
Metsada Pasmanik-Chor
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
User Interface ◽  
High Throughput ◽  
Graphical User Interface ◽  
Differential Expression Analysis ◽  
Biological Data ◽  
Expression Data ◽  
Batch Correction ◽  
User Friendly

This article describes how the last decade has been characterized by the production of huge amounts of different types of biological data. Following that, a flood of bioinformatics tools have been published. However, many of these tools are commercial, or require computational skills. In addition, not all tools provide intuitive and highly accessible visualization of the results. The authors have developed GEView (Gene Expression View), which is a free, user-friendly tool harboring several existing algorithms and statistical methods for the analysis of high-throughput gene, microRNA or protein expression data. It can be used to perform basic analysis such as quality control, outlier detection, batch correction and differential expression analysis, through a single intuitive graphical user interface. GEView is unique in its simplicity and highly accessible visualization it provides. Together with its basic and intuitive functionality it allows Bio-Medical scientists with no computational skills to independently analyze and visualize high-throughput data produced in their own labs.

scholarly journals Implementation of Pll in Rf Transceiver using SPI and Uart Protocols

2019 ◽  
Vol 8 (4) ◽  
pp. 10020-10024
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Software Defined Radio ◽  
Vital Role ◽  
Rf Transceiver ◽  
Development Environment ◽  
Integrated Development ◽  
Data Format ◽  
Cross Platform ◽  
Serial Peripheral Interface

Software Defined Radio plays vital role in many applications as the components in it are software selectable. We can select desired frequency and modulation technique which can be selected through software. The desired frequency selected should be locked in phase locked loop (PLL). The desired frequency is selected by giving commands from Graphical User Interface (GUI) using Universal Asynchronous Receiver Transmitter (UART) and Serial Peripheral Interface (SPI) protocols.GUI is created using Qt creator which is a cross platform C++ and java script Integrated Development Environment (IDE). GUI is designed to generate the desired frequency. As soon as we select a frequency, the corresponding address and data are generated to configure in the Radio Frequency (RF) transceiver. These address and data are first sent to the PIC microcontroller by communicating through UART protocol and after setting data format, these are sent from Peripheral Interface Controller (PIC) to RF transceiver by communicating through SPI protocol. With this process, the registers in RF transceiver are controlled by the user

Information Visualization and Interface Culture

2011 ◽  
pp. 196-212
Author(s):  
Greg J. Smith
Keyword(s):  
User Interface ◽  
Visual Culture ◽  
20Th Century ◽  
Information Visualization ◽  
Graphical User Interface ◽  
Information Design ◽  
History Of ◽  
Information Aesthetics ◽  
History And Theory

This text seeks to contextualize the history of and discourse surrounding information visualization. It positions visualization in relation to broader 20th century visual culture and addresses the evolution of the interface as a ubiquitous tool and the aesthetics for understanding the organization of information. A timeline of precursors to the Graphical User Interface (GUI) is developed and a survey of recent related history and theory is conducted to deliver additional perspectives on information aesthetics. The text concludes with a brief survey of several recent visualization projects to illustrate the variety of fields being engaged and enriched by contemporary information design.

Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night

2018 ◽  
Vol 16 (01) ◽  
pp. 1740011 ◽  
Author(s):  
Olga Kiseleva ◽  
Ekaterina Poverennaya ◽  
Alexander Shargunov ◽  
Andrey Lisitsa
Keyword(s):  
User Interface ◽  
Open Source ◽  
High Throughput ◽  
Graphical User Interface ◽  
Modern Science ◽  
Human Proteome ◽  
Tandem Ms ◽  
Report Generation ◽  
Manual Search ◽  
Human Proteins

Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the “speed” of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui.googlecode.com ) into total result of proteoforms identification and optimized set of engines working simultaneously. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. We selected combination of X!Tandem, MS-GF[Formula: see text] and OMMSA as the most time-efficient and productive combination of search. We added homemade java-script to automatize pipeline from file picking to report generation. These settings resulted in rise of the efficiency of our customized pipeline unobtainable by manual scouting: the analysis of 192 files searched against human proteome (42153 entries) downloaded from UniProt took 11[Formula: see text]h.

scholarly journals Polo: an open-source graphical user interface for crystallization screening

2021 ◽  
Vol 54 (2) ◽  
Author(s):  
Ethan T. Holleman ◽  
Erica Duguid ◽  
Lisa J. Keefe ◽  
Sarah E. J. Bowman
Keyword(s):  
Neural Network ◽  
Crystal Growth ◽  
User Interface ◽  
High Throughput ◽  
Graphical User Interface ◽  
Graphical Interface ◽  
Commercial Use ◽  
Crystallization Experiments ◽  
Crystallization Conditions ◽  
General Public License

Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to efficiently inspect their crystallization experiments. Polo aims to increase efficiency, reducing time spent manually reviewing crystallization images, and to improve the potential of identifying positive crystallization conditions. Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes (MARCO) convolutional neural network for automated image classification, as well as powerful tools to view and score crystallization images, to compare crystallization conditions, and to facilitate collaborative review of crystallization screening results. Crystallization images need not have been captured at HWI to utilize Polo's basic functionality. Polo is free to use and modify for both academic and commercial use under the terms of the copyleft GNU General Public License v3.0.

scholarly journals FusionViewer: An Open Source Toolkit for Viewing Multimodality Images

2008 ◽  
Author(s):  
Yi Lu ◽  
Chris Lau ◽  
Lydia Ng ◽  
Lixin Gong ◽  
Paul Kinahan ◽  
...  
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Image Display ◽  
Ct Image ◽  
Pet Ct ◽  
Cross Platform ◽  
Line Measure ◽  
Anatomical Information ◽  
Ct Studies

FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) facilitates efficient visualization and analysis of PET/CT studies via different viewing modes (linked cursor display, alpha-blend mode, checkerboard mode and split window mode). FusionViewer is implemented in Java and uses the Java OpenGL (JOGL) library and the Insight Segmentation and Registration Toolkit (ITK) library, which make it both a fast and cross-platform application. Its intuitive graphical user interface makes it easy to be used by physicians, radiologists, and research scientists. Several analysis and display tools are already available (navigator, zoom, pan, screen snapshot, ROI, and line measure tool; alpha-blending, checkerboard display, and split window display). Along with PET/CT, several other modalities where co-registered images are often visualized simultaneously have benefited from the use of this software.

Intelligent Fault Diagnosis at the Australia Telescope

1994 ◽  
Vol 11 (2) ◽  
pp. 180-187
Author(s):  
Robert Landau
Keyword(s):  
User Interface ◽  
Fault Diagnosis ◽  
Graphical User Interface ◽  
Failure Modes ◽  
Robust Regression ◽  
Signal Pathways ◽  
History Of ◽  
Small Set ◽  
Monitor Data ◽  
Interactive Graphical User Interface

AbstractThe Fault Diagnosis Expert System for the Australia Telescope analyses ~12000 items of monitor data every minute that report the health and stability of specific components and signal pathways in the array. These data are divided into signatures which are matched against signatures of known failure modes to diagnose problems with the array. Knowledge about many of the failures is acquired by generating them in earlier tests. The system keeps a six-hour history of the detailed behaviour of all monitor data as well as the visibilities. It archives the data in half-hour intervals, characterising the interval with a small set of robust statistical estimators. An interactive graphical user interface allows the simultaneous display of twenty-four histories of either the 6-hour data or one week of the characterised data, together with options for plotting one history against another and for calculating their robust regression.

scholarly journals The Bayesian New Statistics (Public)

2017 ◽  
Author(s):  
John K. Kruschke ◽  
Torrin Liddell
Keyword(s):  
Hypothesis Testing ◽  
Bayesian Methods ◽  
Meta Analysis ◽  
Bayesian Approaches ◽  
Randomized Controlled ◽  
Credible Intervals ◽  
Conceptual Distinction ◽  
The One ◽  
New Statistics ◽  
Better Than

In the practice of data analysis, there is a conceptual distinction between hypothesis testing, on the one hand, and estimation with quantified uncertainty, on the other hand. Among frequentists in psychology a shift of emphasis from hypothesis testing to estimation has been dubbed "the New Statistics" (Cumming, 2014). A second conceptual distinction is between frequentist methods and Bayesian methods. Our main goal in this article is to explain how Bayesian methods achieve the goals of the New Statistics better than frequentist methods. The article reviews frequentist and Bayesian approaches to hypothesis testing and to estimation with confidence or credible intervals. The article also describes Bayesian approaches to meta-analysis, randomized controlled trials, and power analysis.

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