A Visualization Tool for Relationship between Source Code and Parse Tree Using VR

2020 ◽  
Author(s):  
Masateru Kishikawa ◽  
Tetsuro Kakeshita
Keyword(s):  
Source Code ◽  
Parse Tree ◽  
Visualization Tool

scholarly journals CLINE: a web-tool for the comparison of biological dendrogram structures

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rodolfo S. Allendes Osorio ◽  
Lokesh P. Tripathi ◽  
Kenji Mizuguchi
Keyword(s):  
User Interface ◽  
Open Access ◽  
Special Interest ◽  
Web Application ◽  
Source Code ◽  
Visualization Tool ◽  
Web Tool ◽  
Link Type ◽  
Multiple Structures ◽  
Biological Interpretation

Abstract Background When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the dendrogram structure caused by permuting biological replicates, do not necessarily imply a different biological interpretation. Here, we introduce a visualization tool to help identify biologically similar topologies across different clustering results, even in the presence of replicates. Results Here we introduce CLINE, an open-access web application that allows users to visualize and compare multiple dendrogram structures, by visually displaying the links between areas of similarity across multiple structures. Through the use of a single page and a simple user interface, the user is able to load and remove structures form the visualization, change some aspects of their display and set the parameters used to match cluster topology across consecutive pairs of dendrograms. Conclusions We have implemented a web-tool that allows the users to visualize different dendrogram structures, showing not only the structures themselves, but also linking areas of similarity across multiple structures. The software is freely available at http://mizuguchilab.org/tools/cline/. Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/.

scholarly journals PDV: an integrative proteomics data viewer

2018 ◽  
Vol 35 (7) ◽  
pp. 1249-1251 ◽  
Author(s):  
Kai Li ◽  
Marc Vaudel ◽  
Bing Zhang ◽  
Yan Ren ◽  
Bo Wen
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Source Code ◽  
Peptide Identification ◽  
Supplementary Information ◽  
Visualization Tool ◽  
Command Line ◽  
Proteomics Data ◽  
Desktop Computers ◽  
Wide Range

Abstract Summary Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation of peptide identification results. Herein, we present PDV, an integrative proteomics data viewer that can be used to visualize a wide range of proteomics data, including database search results, de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from public proteomics repositories. PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes. Availability and implementation PDV software and the user manual are freely available at http://pdv.zhang-lab.org. The source code is available at https://github.com/wenbostar/PDV and is released under the GPL-3 license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals KWMeshVisu: A Mesh Visualization Tool for Shape Analysis

2006 ◽  
Author(s):  
Ipek Oguz ◽  
Guido Gerig ◽  
Sebastien BARRE ◽  
Martin Styner
Keyword(s):  
Shape Analysis ◽  
Source Code ◽  
Qualitative Evaluation ◽  
Covariance Matrices ◽  
P Value ◽  
Visualization Tool ◽  
Local Covariance ◽  
Statistical Shape ◽  
Visualization Toolkit ◽  
Statistical Results

Many statistical shape analysis methods produce various types of data about the analyzed surfaces, such as p-value maps, distance maps, 3D difference vectors and local covariance matrices. This data is often too large and thus difficult to be properly evaluated on a qualitative basis. A visual representation of this data strongly simplifies qualitative evaluation by humans and thus greatly enhances the value of the statistical results. In this paper we present a new tool for visualizing various datasets on surfaces represented as triangle meshes. Our tool, KWMeshVisu, is implemented using the Insight Toolkit ITK, www.itk.org, the Visualization Toolkit VTK, www.vtk.org, and the KWWidgets user interface toolkit, www.kwwidgets.org. The source code for KWMeshVisu, as well as input data used to generate the images in this paper, is provided with this document.

An application for plagiarized source code detection based on a parse tree kernel

2013 ◽  
Vol 26 (8) ◽  
pp. 1911-1918 ◽  
Author(s):  
Jeong-Woo Son ◽  
Tae-Gil Noh ◽  
Hyun-Je Song ◽  
Seong-Bae Park
Keyword(s):  
Source Code ◽  
Parse Tree ◽  
Tree Kernel

scholarly journals A Visualization Tool for Analyzing the Suitability of Software Libraries via Their Code Repositories

2020 ◽  
Vol 2020 (1) ◽  
pp. 387-1-387-11
Author(s):  
Casey Haber ◽  
Robert Gove
Keyword(s):  
User Interface ◽  
Source Code ◽  
Visualization Tool ◽  
Software Library ◽  
Software Libraries ◽  
Key Aspects

Code repositories are a common way to archive software source code files. Understanding code repository content and history is important but can be difficult due to the complexity of code repositories. Most available tools are designed for users who are actively maintaining a code repository. In contrast, external developers need to assess the suitability of using a software library, e.g. whether its code repository has a healthy level of maintenance, and how much risk the external developers face if they depend on that code in their own project. In this paper, we identify six risks associated with using a software library, we derive seven requirements for tools to assess these risks, and we contribute two dashboard designs derived from these requirements. The first dashboard is designed to assess a software library's usage suitability via its code repository, and the second dashboard visually compares usage suitability information about multiple software libraries' code repositories. Using four popular libraries' code repositories, we show that these dashboards are effective for understanding and comparing key aspects of software library usage suitability. We further compare our dashboard to a typical code repository user interface and show that our dashboard is more succinct and requires less work.

scholarly journals VTrace-A Tool for Visualizing Traceability Links among Software Artefacts for an Evolving System

2017 ◽  
Vol 6 (2) ◽  
pp. 201-218
Author(s):  
C J Satish ◽  
Anand M
Keyword(s):  
Change Management ◽  
Impact Analysis ◽  
Source Code ◽  
Maintenance Phase ◽  
Software Project ◽  
Visualization Tool ◽  
Development Phase ◽  
Development Stages ◽  
Evolving System ◽  
The Impact

Traceability Management plays a key role in tracing the life of a requirement through all the specifications produced during the development phase of a software project. A lack of traceability information not only hinders the understanding of the system but also will prove to be a bottleneck in the future maintenance of the system. Projects that maintain traceability information during the development stages somehow fail to upgrade their artefacts or maintain traceability among the different versions of the artefacts that are produced during the maintenance phase. As a result the software artefacts lose the trustworthiness and engineers mostly work from the source code for impact analysis. The goal of our research is on understanding the impact of visualizing traceability links on change management tasks for an evolving system. As part of our research we have implemented a Traceability Visualization Tool-VTrace that manages software artefacts and also enables the visualization of traceability links. The results of our controlled experiment show that subjects who used the tool were more accurate and faster on change management tasks than subjects that didn’t use the tool.

scholarly journals A Visualization Tool for Analyzing the Suitability of Software Libraries via Their Code Repositories

2019 ◽  
Author(s):  
Casey Haber ◽  
Robert Gove
Keyword(s):  
User Interface ◽  
Source Code ◽  
Visualization Tool ◽  
Software Library ◽  
Software Libraries ◽  
Key Aspects

Code repositories are a common way to archive software source code files. Understanding code repository content and his- tory is important but can be difficult due to the complexity of code repositories. Most available tools are designed for users who are actively maintaining a code repository. In contrast, external developers need to assess the suitability of using a software library, e.g. whether its code repository has a healthy level of maintenance, and how much risk the external developers face if they depend on that code in their own project. In this paper, we identify six risks associated with using a software library, we derive seven requirements for tools to assess these risks, and we con- tribute two dashboard designs derived from these requirements. The first dashboard is designed to asses a software library's usage suitability via its code repository, and the second dashboard visually compares usage suitability information about multiple soft- ware libraries’ code repositories. Using four popular libraries code repositories, we show that these dashboards are effective for understanding and comparing key aspects of software library us- age suitability. We further compare our dashboard to a typical code repository user interface and show that our dashboard is more succinct and requires less work.

scholarly journals Computation of Program Source Code Similarity by Composition of Parse Tree and Call Graph

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Hyun-Je Song ◽  
Seong-Bae Park ◽  
Se Young Park
Keyword(s):  
Structural Information ◽  
Source Code ◽  
Real Data ◽  
Kernel Functions ◽  
Parse Tree ◽  
Plagiarism Detection ◽  
Data Set ◽  
Source Codes ◽  
Function Calls ◽  
Syntactic Information

This paper proposes a novel method to compute how similar two program source codes are. Since a program source code is represented as a structural form, the proposed method adopts convolution kernel functions as a similarity measure. Actually, a program source code has two kinds of structural information. One is syntactic information and the other is the dependencies of function calls lying on the program. Since the syntactic information of a program is expressed as its parse tree, the syntactic similarity between two programs is computed by a parse tree kernel. The function calls within a program provide a global structure of a program and can be represented as a graph. Therefore, the similarity of function calls is computed with a graph kernel. Then, both structural similarities are reflected simultaneously into comparing program source codes by composing the parse tree and the graph kernels based on a cyclomatic complexity. According to the experimental results on a real data set for program plagiarism detection, the proposed method is proved to be effective in capturing the similarity between programs. The experiments show that the plagiarized pairs of programs are found correctly and thoroughly by the proposed method.

scholarly journals FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data

2020 ◽  
Author(s):  
Simon Leonard ◽  
Antoine Rolland ◽  
Karin Tarte ◽  
Frédéric Chalmel ◽  
Aurélie Lardenois
Keyword(s):  
Single Cell ◽  
Source Code ◽  
R Package ◽  
Quantitative Information ◽  
Visualization Tool ◽  
Visualization Method ◽  
Rna Seq ◽  
Shiny App ◽  
R Shiny ◽  
Shiny Application

AbstractMotivationDot plots are heatmap-like charts that provide a compact way to simultaneously display two quantitative information by means of dots of different sizes and colours. Despite the popularity of this visualization method, particularly in single-cell RNA-seq studies, existing tools used to make dot plots are limited in terms of functionality and usability.ResultsWe developed FlexDotPlot, an R package for generating dot plots from any type of multifaceted data, including single-cell RNA-seq data. FlexDotPlot provides a universal and easy-to-use solution with a high versatility. An interactive R Shiny application is also available in the FlexDotPlot package allowing non-R users to easily generate dot plots with several tunable parameters.Availability and implementationSource code and detailed manual are available at https://github.com/Simon-Leonard/FlexDotPlot. The Shiny app is available as a stand-alone application within the package.

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