scholarly journals karyoploteR: an R/Bioconductor package to plot customizable linear genomes displaying arbitrary data

2017 ◽  
Author(s):  
Bernat Gel ◽  
Eduard Serra
Keyword(s):  
Experimental Data ◽  
Source Code ◽  
Genomic Data ◽  
Data Exploration ◽  
Main Function ◽  
Bioconductor Package ◽  
End User ◽  
Creation Process ◽  
Whole Genomes ◽  
Linear Genomes

AbstractMotivationData visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species.ResultsWe have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation.AvailabilitykaryoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR)[email protected]

Expert and Novice End-User Spreadsheet Debugging

2011 ◽  
Vol 23 (2) ◽  
pp. 57-80 ◽  
Author(s):  
Brian Bishop ◽  
Kevin McDaid
Keyword(s):  
Experimental Data ◽  
Real World ◽  
End Users ◽  
End User ◽  
Novel Approach ◽  
Expert And Novice ◽  
Research Studies

The reliability of end-user developed spreadsheets is poor. Research studies find that 94% of ‘real-world’ spreadsheets contain errors. Although some research has been conducted in the area of spreadsheet testing, little is known about the behaviour or processes of individuals during the debugging task. In this paper, the authors investigate the performance and behaviour of expert and novice end-users in the debugging of an experimental spreadsheet. To achieve this aim, a spreadsheet debugging experiment was conducted, with professional and student participants requested to debug a spreadsheet seeded with errors. The work utilises a novel approach for acquiring experimental data through the unobtrusive recording of participants’ actions using a custom built VBA tool. Based on findings from the experiment, a debugging tool is developed, and its effects on debugging performance are investigated.

scholarly journals An Expert Judgment in Source Code Quality Research Domain—A Comparative Study between Professionals and Students

2020 ◽  
Vol 10 (20) ◽  
pp. 7088
Author(s):  
Luka Pavlič ◽  
Marjan Heričko ◽  
Tina Beranič
Keyword(s):  
Experimental Data ◽  
Software Engineering ◽  
Research Evidence ◽  
Source Code ◽  
Scientific Research ◽  
Controlled Experiments ◽  
Quality Research ◽  
Professional Responses ◽  
Code Quality ◽  
Research Domain

In scientific research, evidence is often based on empirical data. Scholars tend to rely on students as participants in experiments in order to validate their thesis. They are an obvious choice when it comes to scientific research: They are usually willing to participate and are often themselves pursuing an education in the experiment’s domain. The software engineering domain is no exception. However, readers, authors, and reviewers do sometimes question the validity of experimental data that is gathered in controlled experiments from students. This is why we will address this difficult-to-answer question: Are students a proper substitute for experienced professional engineers while performing experiments in a typical software engineering experiment. As we demonstrate in this paper, it is not a “yes or no” answer. In some aspects, students were not outperformed by professionals, but in others, students would not only give different answers compared to professionals, but their answers would also diverge. In this paper we will show and analyze the results of a controlled experiment in the source code quality domain in terms of comparing student and professional responses. We will show that authors have to be careful when employing students in experiments, especially when complex and advanced domains are addressed. However, they may be a proper substitution in cases, where non-advanced aspects are required.

scholarly journals tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes

2020 ◽  
Vol 36 (11) ◽  
pp. 3597-3599 ◽  
Author(s):  
Iurii S Nagornov ◽  
Mamoru Kato
Keyword(s):  
Cancer Cell ◽  
Tumor Heterogeneity ◽  
Clonal Evolution ◽  
Source Code ◽  
Genomic Data ◽  
Supplementary Information ◽  
Cell Behavior ◽  
Supplementary Data ◽  
Hallmarks Of Cancer ◽  
Cell Evolution

Abstract Summary The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. Availability and implementation The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals TcruziKB: Enabling Complex Queries for Genomic Data Exploration

2008 ◽  
Author(s):  
Pablo N. Mendes ◽  
Bobby McKnight ◽  
Amit P. Sheth ◽  
Jessica C. Kissinger
Keyword(s):  
Genomic Data ◽  
Data Exploration ◽  
Complex Queries

scholarly journals DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

2021 ◽  
Author(s):  
Almut Heinken ◽  
Stefanía Magnúsdóttir ◽  
Ronan M T Fleming ◽  
Ines Thiele
Keyword(s):  
Experimental Data ◽  
Draft Genome ◽  
Genomic Data ◽  
Quality Standards ◽  
Gene Annotations ◽  
Manual Curation ◽  
Genome Annotations ◽  
Species Specific ◽  
Genome Scale ◽  
Cobra Toolbox

Abstract Motivation Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account. Results We developed DEMETER, a COBRA Toolbox extension, that enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data, and refinement of pathways based on manually refined genome annotations. Availability DEMETER and tutorials are freely available at https://github.com/opencobra.

scholarly journals Mathematical Modeling of Closed Loop Pulsating Heat Pipe by Using Artificial Neural Networks

2021 ◽  
Vol 39 (3) ◽  
pp. 955-962
Author(s):  
Santhi Sree Nerella ◽  
Sudheer V.V.S. Nakka ◽  
Bhramara Panitapu
Keyword(s):  
Neural Network ◽  
Experimental Data ◽  
Heat Pipe ◽  
Closed Loop ◽  
Analytical Models ◽  
System Modelling ◽  
Main Function ◽  
Pulsating Heat Pipe ◽  
Condenser Section ◽  
Artificial Neural

Pulsating heat pipe is one of the prominent technology for thermal management of electronic devices. It consists of three sections namely evaporator, adiabatic and condenser section. PHP is a two phase passive device having efficient and quick ability of transferring heat from evaporator section to condenser section. At first an 8 turn pulsating heat pipe of closed loop ends (CLPHP) with copper tube capillary dimensions is investigated experimentally for different fill ratios and for different inclinations by varying range of heat inputs. Different working fluids viz Water, Acetone, Ethanol and Methanol are considered for the experimentation. One of the recent analytical technology for modelling of CLPHPs is Artificial Neural Network (ANN) approach. The analytical models are having limited scope of applicability and they are simple in nature. The present paper describes Validation of experimental data by training prediction model ANN with available data. Three input nodes such as input heat, fill ratio and angle of inclination and one output node corresponding to PHP that is thermal resistance are considered. The feed forward neural network (FFNN) architecture is adopted for predictions. By using the physical phenomena of the system modelling are clearly known for obtaining feasible results which is main function of ANN. The predicted data validates experimental data in a satisfactory range and the results are found to be in good agreement with in the range of ± 10 percent.

scholarly journals Method and program for the interpolation of experimental results of determining the mechanical properties of mineral composites for modern machine–tools

2019 ◽  
Vol 299 ◽  
pp. 05009
Author(s):  
Mihai Ciupan ◽  
Marcel Popa ◽  
Emilia Ciupan
Keyword(s):  
Experimental Data ◽  
Mechanical Properties ◽  
Machine Tools ◽  
Source Code ◽  
Experimental Results ◽  
Independent Variables ◽  
Input And Output ◽  
Matlab Program ◽  
Modern Machine ◽  
Data Plotting

The paper presents a method of interpolating bifactorial experimental data with the aim of extending the results over the entire domain defined by the independent variables. This approach can be used in determining the optimum mineral casting mixes for a given application. Mechanical properties such as stiffness, ultimate tensile strength, yield strength and Poisson's coefficient can be improved.The paper describes the implementation of a radial basis function (RBF) algorithm in a MATLAB program for the interpolation of data, plotting of the results and the identification of the maximum dependent variable and the independent variables that correspond to it. It also provides the source code for the program along with explanations regarding its use. RBF interpolations can be used successfully in response surface methodology to generate approximations of the studied variables based on the experimental results. The program can be extended to work on any number of input and output variables.

scholarly journals HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data

2016 ◽  
Vol 32 (15) ◽  
pp. 2372-2374 ◽  
Author(s):  
Zuguang Gu ◽  
Roland Eils ◽  
Matthias Schlesner
Keyword(s):  
High Resolution ◽  
Genomic Data ◽  
Bioconductor Package

The Study of Planar Five-Bar Parallel Robot Dynamic Characteristics

2012 ◽  
Vol 468-471 ◽  
pp. 954-958
Author(s):  
Shang Yue Chen ◽  
Hong Bing Xin ◽  
Han Ning Mo ◽  
Mei Yu Chen ◽  
Dong Yang Zhao
Keyword(s):  
Experimental Data ◽  
Control System ◽  
Frequency Domain ◽  
Dynamic Characteristics ◽  
Parallel Robot ◽  
Robot Dynamics ◽  
Main Function ◽  
Vibration Acceleration ◽  
Experimental Purpose ◽  
End Effectors

By introducing the experimental purpose, instruments and the main function of the planar five-bar parallel robot dynamics, this paper concluded the principle diagram of control system of the planar five-bar parallel robot. And the method and process of the experiment was detailed description. Through the analysis of vibration acceleration curve and frequency domain curve, which were obtained by the experimental data of the planar five-bar parallel robot end-effectors, the characteristics of time and frequency domain of the planar five-bar parallel robot were clearly shown.

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