Journal articles: 'Source code visualization'

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Jakobsen, Mikkel Rønne, and Kasper Hornbæk. "Transient or permanent fisheye views: A comparative evaluation of source code interfaces." Information Visualization 11, no. 2 (July 18, 2011): 151–67. http://dx.doi.org/10.1177/1473871611405643.

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Transient use of information visualization may support specific tasks without permanently changing the user interface. Transient visualizations provide immediate and transient use of information visualization close to and in the context of the user’s focus of attention. Little is known, however, about the benefits and limitations of transient visualizations. We describe an experiment that compares the usability of a fisheye view that participants could call up temporarily, a permanent fisheye view, and a linear view: all interfaces gave access to source code in the editor of a widespread programming environment. Fourteen participants performed varied tasks involving navigation and understanding of source code. Participants used the three interfaces for between four and six hours in all. Time and accuracy measures were inconclusive, but subjective data showed a preference for the permanent fisheye view. We analyse interaction data to compare how participants used the interfaces and to understand why the transient interface was not preferred. We conclude by discussing seamless integration of fisheye views in existing user interfaces and future work on transient visualizations.

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Al-Msie'deen, R. A. "Tag Clouds for Object-Oriented Source Code Visualization." Engineering, Technology & Applied Science Research 9, no. 3 (June 8, 2019): 4243–48. http://dx.doi.org/10.48084/etasr.2706.

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Software visualization helps software engineers to understand and manage the size and complexity of the object-oriented source code. The tag cloud is a simple and popular visualization technique. The main idea of the tag cloud is to represent tags according to their frequency in an alphabetical order where the most important tags are highlighted via a suitable font size. This paper proposes an original approach to visualize software code using a tag cloud. The approach exploits all software identifier names to visualize software code as a tag cloud. Experiments were conducted on several case studies. To validate the approach, it is applied on NanoXML and ArgoUML. The results of this evaluation validate the relevance and the performance of the proposed approach as all tag names and their frequencies were correctly identiﬁed. The proposed tag cloud visualization technique is a helpful addition to the software visualization toolkit. The extracted tag cloud supports software engineers as they filter and browse data.

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Kadar, Rozita, Jamal Othman, and Naemah Abdul Wahab. "Survey on Ontology-Based Visualization Techniques towards Program Comprehension Application." Journal of Computing Research and Innovation 3, no. 1 (October 17, 2018): 19–29. http://dx.doi.org/10.24191/jcrinn.v3i1.66.

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A key challenge to software maintainers during performing the software maintenance is to comprehend a source code. Source code plays an important role in aiding software maintainers to get conversant with a software system since some system documentations are often unavailable or outdated. Although there are many researches that have discussed the different strategies and techniques to overcome the program comprehension problem, there exists only a shallow knowledge about the challenges software maintainers face when trying to understand a software system through reading source code. In order to make source code more comprehensible, it needs to make an enhancement regarding to the source code presentation by transforming it into a different view. From the literature review, we found that there are lacks of study that consider the use of knowledge representation to represent source code. Hence, the aim of this work is to review the existing techniques for source code representation based on knowledge representation that could help developers to reduce the amount of their effort needed to understand a source code.

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Luo, Yi, and Yanying Han. "Source Code Visualization in Linux Environment Based on Hierarchica Layout Algorithm." Information Technology Journal 12, no. 8 (April 1, 2013): 1522–30. http://dx.doi.org/10.3923/itj.2013.1522.1530.

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ISHIDA, Naoto, Takashi ISHIO, Yuta NAKAMURA, Shinji KAWAGUCHI, Tetsuya KANDA, and Katsuro INOUE. "Visualization of Inter-Module Dataflow through Global Variables for Source Code Review." IEICE Transactions on Information and Systems E101.D, no. 12 (December 1, 2018): 3238–41. http://dx.doi.org/10.1587/transinf.2018edl8104.

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Ovchinnikova, Viktoria. "Obtaining and Visualization of the Topological Functioning Model from the UML Model." Applied Computer Systems 18, no. 1 (December 1, 2015): 43–51. http://dx.doi.org/10.1515/acss-2015-0018.

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Abstract A domain model can provide compact information about its corresponding software system for business people. If the software system exists without its domain model and documentation it is time-consuming to understand its behavior and structure only from the code. Reverse Engineering (RE) tools can be used for obtaining behavior and structure of the software system from source code. After that the domain model can be created. A short overview and an example of obtaining the domain model, Topological Functioning Model (TFM), from source code are provided in the paper. Positive and negative effects of the process of TFM backward derivation are also discussed.

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Wan, Ying, Chuan Qi Tan, Zhi Gang Wang, Guo Qiang Wang, and Xiao Jin Hong. "An Effective Visual System for Static Analysis of Source Code." Advanced Materials Research 433-440 (January 2012): 5453–58. http://dx.doi.org/10.4028/www.scientific.net/amr.433-440.5453.

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In the software development lifecycle, code static analysis takes an important part in building secure software. To help discover the potential security issues in source code, large numbers of static analysis tools are developed. But the results generated by them display in the form of pure text, so it is time-consuming for developers to analyze these text messages, and it is difficult for developers to concentrate on the most interesting defects in huge data. In this paper, we have developed a visualization system oriented to Java source code, which presents the results in graphics from a developer’s point of view, to help developers to analysis code defects. A novel layout is proposed to visualize software source code in a hierarchy way, which shows the physical structure of the software. A visual overview and powerful interaction is provided in this system which allows the developer to focus on the most pressing defects within huge volumes of source code.

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Cruz, da, Rangel Henriques, and João Varanda. "Constructing program animations using a pattern based approach." Computer Science and Information Systems 4, no. 2 (2007): 97–114. http://dx.doi.org/10.2298/csis0702097c.

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The aim of this paper is to discuss how our pattern-based strategy for the visualization of data and control flow can effectively be used to animate the program and exhibit its behavior. That result allows us to propose its use for Program Comprehension. The animator uses well known compiler techniques to inspect the source code in order to extract the necessary information to visualize it and understand program execution. We convert the source program into an internal decorated (or attributed) abstract syntax tree and then we visualize the structure by traversing it, and applying visualization rules at each node according to a pre-defined rule-base. In order to calculate the next step in the program execution, a set of rewriting rules are applied to the tree. The visualization of this new tree is shown and the program animation is constructed using an iterative process. No changes are made in the source code, and the execution is simulated step by step. Several examples of visualization are shown to illustrate the approach and support our idea of applying it in the context of a Program Comprehension environment.

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Grivainis, Mark, Zuojian Tang, and David Fenyö. "TranspoScope: interactive visualization of retrotransposon insertions." Bioinformatics 36, no. 12 (April 16, 2020): 3877–78. http://dx.doi.org/10.1093/bioinformatics/btaa244.

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Abstract Motivation Retrotransposition is an important force in shaping the human genome and is involved in prenatal development, disease and aging. Current genome browsers are not optimized for visualizing the experimental evidence for retrotransposon insertions. Results We have developed a specialized browser to visualize the evidence for retrotransposon insertions for both targeted and whole-genome sequencing data. Availability and implementation TranspoScope’s source code, as well as installation instructions, are available at https://github.com/FenyoLab/transposcope.

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Alamin M, Hind, and Hany H. Ammar. "Concerns-Based Reverse Engineering for Partial Software Architecture Visualization." JOIV : International Journal on Informatics Visualization 4, no. 2 (May 26, 2020): 58. http://dx.doi.org/10.30630/joiv.4.2.357.

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Recently, reverse engineering (RE) is becoming one of the essential engineering trends for software evolution and maintenance. RE is used to support the process of analyzing and recapturing the design information in legacy systems or complex systems during the maintenance phase. The major problem stakeholders might face in understanding the architecture of existing software systems is that the knowledge of software architecture information is difficult to obtain because of the size of the system, and the existing architecture document often is missing or does not match the current implementation of the source code. Therefore, much more effort and time are needed from multiple stakeholders such as developers, maintainers and architects for obtaining and re-documenting and visualizing the architecture of a target system from its source code files. The current works is mainly focused on the developer viewpoint. In this paper, we present a RE methodology for visualizing architectural information for multiple stakeholders and viewpoints based on applying the RE process on specific parts of the source code. The process is driven by eliciting stakeholders’ concerns on specific architectural viewpoints to obtain and visualize architectural information related these concerns. Our contributions are three fold: 1- The RE methodology is based on the IEEE 1471 standard for architectural description and supports concerns of stakeholder including the end-user and maintainer; 2- It supports the visualization of a particular part of the target system by providing a visual model of the architectural representation which highlights the main components needed to execute specific functionality of the target system, 3- The methodology also uses architecture styles to organize the visual architecture information. We illustrate the methodology using a case study of a legacy web application system.

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Marschallinger, R. "Three-dimensional reconstruction and visualization of geological materials with IDL — examples and source code." Computers & Geosciences 27, no. 4 (May 2001): 419–26. http://dx.doi.org/10.1016/s0098-3004(00)00126-6.

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Fonna, Syarizal, M. Ridha, S. Huzni, Ahmad Kamal Ariffin, and Israr. "Pre and Post Processing for Boundary Element Method (BEM) 3D Reinforced Concrete Corrosion Simulation." Key Engineering Materials 462-463 (January 2011): 230–35. http://dx.doi.org/10.4028/www.scientific.net/kem.462-463.230.

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Corrosion simulation of rebar in concrete structures using BEM 3D have been developed. However, pre processing procedure such as geometry development and meshing is still performed manually. In addition, the visualization of BEM simulation results is still illustrated using the simple chart and graph. Nowadays, many softwares have been developed under open source platform that can be used freely. There is open source softwares for CAE purposes such as Salome and VisIt. The aim of this study is to implement the open source software as pre- and post-processing for the developed BEM 3D code in order to simulate corrosion of reinforced concrete. Salome 2.3.9 is used for developing geometry and meshing the model. The visualization of the simulation results are conducted using VisIt 1.8. The study shows that the open source software i.e. Salome and VisIt, perform well as pre and post processing of developed code for simulating the corrosion of reinforced concrete. It shows that the meshing procedure and the interpretation of results become simpler and easier.

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Haber, Casey, and Robert Gove. "A Visualization Tool for Analyzing the Suitability of Software Libraries via Their Code Repositories." Electronic Imaging 2020, no. 1 (January 26, 2020): 387–1. http://dx.doi.org/10.2352/issn.2470-1173.2020.1.vda-387.

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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.

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Kwon, Jin-Wook, Yun-Ja Choi, and Woo-Jin Lee. "Development of Analysis and Visualization Tool for Java Source Code Changes using Reverse Engineering Technique." KIPS Transactions:PartD 19D, no. 1 (February 29, 2012): 39–48. http://dx.doi.org/10.3745/kipstd.2012.19d.1.039.

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Wandell, Brian A., Suelika Chial, and Benjamin T. Backus. "Visualization and Measurement of the Cortical Surface." Journal of Cognitive Neuroscience 12, no. 5 (September 2000): 739–52. http://dx.doi.org/10.1162/089892900562561.

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Much of the human cortical surface is obscured from view by the complex pattern of folds, making the spatial relationship between different surface locations hard to interpret. Methods for viewing large portions of the brain's surface in a single flattened representation are described. The flattened representation preserves several key spatial relationships between regions on the cortical surface. The principles used in the implementations and evaluations of these implementations using artificial test surfaces are provided. Results of applying the methods to structural magnetic resonance measurements of the human brain are also shown. The implementation details are available in the source code, which is freely available on the Internet.

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Walsh, Kieran, Mircea A. Voineagu, Fatemeh Vafaee, and Irina Voineagu. "TDAview: an online visualization tool for topological data analysis." Bioinformatics 36, no. 18 (July 2, 2020): 4805–9. http://dx.doi.org/10.1093/bioinformatics/btaa600.

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Abstract Summary TDAview is an online tool for topological data analysis (TDA) and visualization. It implements the Mapper algorithm for TDA and provides extensive graph visualization options. TDAview is a user-friendly tool that allows biologists and clinicians without programming knowledge to harness the power of TDA. TDAview supports an analysis and visualization mode in which a Mapper graph is constructed based on user-specified parameters, followed by graph visualization. It can also be used in a visualization only mode in which TDAview is used for visualizing the data properties of a Mapper graph generated using other open-source software. The graph visualization options allow data exploration by graphical display of metadata variable values for nodes and edges, as well as the generation of publishable figures. TDAview can handle large datasets, with tens of thousands of data points, and thus has a wide range of applications for high-dimensional data, including the construction of topology-based gene co-expression networks. Availability and implementation TDAview is a free online tool available at https://voineagulab.github.io/TDAview/. The source code, usage documentation and example data are available at TDAview GitHub repository: https://github.com/Voineagulab/TDAview.

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Rakitin, Maksim S., Paul Moeller, Robert Nagler, Boaz Nash, David L. Bruhwiler, Dmitry Smalyuk, Mikhail Zhernenkov, and Oleg Chubar. "Sirepo: an open-source cloud-based software interface for X-ray source and optics simulations." Journal of Synchrotron Radiation 25, no. 6 (October 19, 2018): 1877–92. http://dx.doi.org/10.1107/s1600577518010986.

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Sirepo, a browser-based GUI for X-ray source and optics simulations, is presented. Such calculations can be performed using SRW (Synchrotron Radiation Workshop), which is a physical optics computer code, allowing simulation of entire experimental beamlines using the concept of a `virtual beamline' with accurate treatment of synchrotron radiation generation and propagation through the X-ray optical system. SRW is interfaced with Sirepo by means of a Python application programming interface. Sirepo supports most of the optical elements currently used at beamlines, including recent developments in SRW. In particular, support is provided for the simulation of state-of-the-art X-ray beamlines, exploiting the high coherence and brightness of modern light source facilities. New scientific visualization and reporting capabilities have been recently implemented within Sirepo, as well as automatic determination of electron beam and undulator parameters. Publicly available community databases can be dynamically queried for error-free access to material characteristics. These computational tools can be used for the development and commissioning of new X-ray beamlines and for testing feasibility and optimization of experiments. The same interface can guide simulation on a local computer, a remote server or a high-performance cluster. Sirepo is available online and also within the NSLS-II firewall, with a growing number of users at other light source facilities. Our open source code is available on GitHub.

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Opik, Rain, Toomas Kirt, and Innar Liiv. "Megatrend and Intervention Impact Analyzer for Jobs: A Visualization Method for Labor Market Intelligence." Journal of Official Statistics 34, no. 4 (December 1, 2018): 961–79. http://dx.doi.org/10.2478/jos-2018-0047.

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Abstract This article presents a visual method for representing the complex labor market internal structure from the perspective of similar occupations based on shared skills; and a prototype tool for interacting with the visualization, together with an extended description of graph construction and the necessary data processing for linking multiple heterogeneous data sources. Since the labor market is not an isolated phenomenon and is constantly impacted by external trends and interventions, the presented method is designed to enable adding extra layers of external information. For instance, what is the impact of a megatrend or an intervention on the labor market? Which parts of the labor market are the most vulnerable to an approaching megatrend or planned intervention? A case study analyzing the labor market together with the megatrend of job automation and computerization is presented. The source code of the prototype is released as open source for repeatability.

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Mei, Xin Yun, and Jian Bin Liu. "A Refactoring Framework of Program Model Based on Procedure Blueprint." Applied Mechanics and Materials 198-199 (September 2012): 490–94. http://dx.doi.org/10.4028/www.scientific.net/amm.198-199.490.

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Refactoring has been studied for a long time, especially model refactoring has become the hot spot of research in recent years. However, the difference between source-based refactoring and model-based refactoring makes it hard to keep consistent between the target code and model refactoring operations. To resolve the problem, this paper presents a refactoring framework of program model based on Procedure Blueprint and gives the prototyping tool system of program model refactoring. Through seamless connection source code established by procedure blueprint to program model，the formalized framework unified the refactoring of source-based and program model based. The refactoring framework supports the visualization representation of program model and the validation for behavior preservation of graphics transformation, which reduces the complexity of refactoring analysis and software maintenance costs.

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Villaveces, Jose M., Rafael C. Jimenez, and Bianca H. Habermann. "PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers." F1000Research 3 (February 13, 2014): 44. http://dx.doi.org/10.12688/f1000research.3-44.v1.

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Summary: Protein interaction networks have become an essential tool in large-scale data analysis, integration, and the visualization of high-throughput data in the context of complex cellular networks. Many individual databases are available that provide information on binary interactions of proteins and small molecules. Community efforts such as PSICQUIC aim to unify and standardize information emanating from these public databases. Here we introduce PsicquicGraph, an open-source, web-based visualization component for molecular interactions from PSIQUIC services. Availability: PsicquicGraph is freely available at the BioJS Registry for download and enhancement. Instructions on how to use the tool are available here http://goo.gl/kDaIgZ and the source code can be found at http://github.com/biojs/biojs and DOI:10.5281/zenodo.7709.

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Ishizue, Ryosuke, Hironori Washizaki, Yoshiaki Fukazawa, Sakae Inoue, Yoshiiku Hanai, Masanobu Kanazawa, and Katsushi Namba. "Metrics Visualization Techniques Based on Historical Origins and Functional Layers for Developments by Multiple Organizations." International Journal of Software Engineering and Knowledge Engineering 28, no. 01 (January 2018): 123–47. http://dx.doi.org/10.1142/s0218194018500067.

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Software developments involving multiple organizations such as Open Source Software (OSS)-based projects tend to have numerous defects when one organization develops and another organization edits the program source code files. Developments with complex file creation, modification history (origin), and software architecture (functional layer) are increasing in OSS-based development. As an example, we focus on an Android smart phone and a VirtualBox development project, and propose new visualization techniques for product metrics based on file origin and functional layers. One is the Metrics Area Figure, which can express duplication of edits by multiple organizations intuitively using overlapping figures. The other is Origin City, which was inspired by Code City. It can represent the scale and other measurements, while simultaneously stacking functional layers as 3D buildings. The contributions of our paper are to propose new techniques, implement them as web applications, and share the results of our questionnaire. Our proposed techniques are useful not only to visualize the measured metrics, but also to improve the product quality.

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Solano-Roman, A., C. Cruz-Castillo, D. Offenhuber, and A. Colubri. "NX4: a web-based visualization of large multiple sequence alignments." Bioinformatics 35, no. 22 (June 4, 2019): 4800–4802. http://dx.doi.org/10.1093/bioinformatics/btz457.

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Abstract Summary Multiple Sequence Alignments (MSAs) are a fundamental operation in genome analysis. However, MSA visualizations such as sequence logos and matrix representations have changed little since the nineties and are not well suited for displaying large-scale alignments. We propose a novel, web-based MSA visualization tool called NX4, which can handle genome alignments comprising thousands of sequences. NX4 calculates the frequency of each nucleotide along the alignment and visually summarizes the results using a color-blind friendly palette that helps identifying regions of high genetic diversity. NX4 also provides the user with additional assistance in finding these regions with a ‘focus + context’ mechanism that uses a line chart of the Shannon entropy across the alignment. The tool offers geneticists an easy-to-use and scalable analysis for large MSA studies. Availability and implementation NX4 is freely available at https://www.nx4.io, and its source code at https://github.com/NX4/nx4. Supplementary information Supplementary data are available at Bioinformatics online

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Lazarov, Andon, Dimitar Minchev, and Atanas Dimitrov. "Ultrasonic Positioning System Implementation and Dynamic 3D Visualization." Cybernetics and Information Technologies 17, no. 2 (June 1, 2017): 151–63. http://dx.doi.org/10.1515/cait-2017-0023.

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Abstract The paper contributes to the design and implementation of the ultrasonic positioning system based on new multifunctional hardware components, newly released. A moving object coordinates’ determination is described analytically and a matrix equation in respect to unknown coordinates with coefficients, measurement distances, is derived. Stages of data packet processing are formulated, and a pseudo pyramid of measurement distances is built. HX7TR multifunctional ultrasonic devises, transceivers, are used to implement the positioning system. A C# program source code for coordinate determination and 3D visualization is created. The algorithm for moving object coordinate computation, and its program realization as well as HX7TR ultrasonic devises can be used in development of indoor ultrasonic positioning systems embedded in IoT and robotics applications.

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Bernau, John A. "Text Analysis with JSTOR Archives." Socius: Sociological Research for a Dynamic World 4 (January 2018): 237802311880926. http://dx.doi.org/10.1177/2378023118809264.

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I provide a visual representation of keyword trends and authorship for two flagship sociology journals using data from JSTOR’s Data for Research repository. While text data have accompanied the digital spread of information, it remains inaccessible to researchers unfamiliar with the required preprocessing. The visualization and accompanying code encourage widespread use of this source of data in the social sciences.

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Zhou, Chenliang, Dominic Kuang, Jingru Liu, Hanbo Yang, Zijia Zhang, Alan Mackworth, and David Poole. "AISpace2: An Interactive Visualization Tool for Learning and Teaching Artificial Intelligence." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 09 (April 3, 2020): 13436–43. http://dx.doi.org/10.1609/aaai.v34i09.7068.

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AIspace is a set of tools used to learn and teach fundamental AI algorithms. The original version of AIspace was written in Java. There was not a clean separation of the algorithms and visualization; it was too complicated for students to modify the underlying algorithms. Its next generation, AIspace2, is built on AIPython, open source Python code that is designed to be as close as possible to pseudocode. AISpace2, visualized in JupyterLab, keeps the simple Python code, and uses hooks in AIPython to allow visualization of the algorithms. This allows students to see and modify the high-level algorithms in Python, and to visualize the output in a graphical form, aiming to better help them to build confidence and comfort in AI concepts and algorithms. So far we have tools for search, constraint satisfaction problems (CSP), planning and Bayesian network. In this paper we outline the tools and give some evaluations based on user feedback.

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Elvina, Elvina, Oscar Karnalim, Mewati Ayub, and Maresha Caroline Wijanto. "Combining program visualization with programming workspace to assist students for completing programming laboratory task." Journal of Technology and Science Education 8, no. 4 (June 21, 2018): 268. http://dx.doi.org/10.3926/jotse.420.

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Numerous Program Visualization tools (PVs) have been developed for assisting novice students to understand their source code further. However, none of them are practical to be used in the context of completing programming laboratory task; students are required to keep switching between PV and programming workspace when they need to know how their code works. This paper combines PV with programming workspace to handle such issue. Resulted tool (which is named PITON) has 13 features extracted from PythonTutor, PyCharm, and student’s feedbacks about PythonTutor. According to think-aloud and user study, PITON is more practical to be used than a combination of PythonTutor and PyCharm. Further, its features are considerably helpful; students rated these features as useful and frequently used.

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Dérozier, Sandra, Pierre Nicolas, Ulrike Mäder, and Cyprien Guérin. "Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations." Bioinformatics 37, no. 17 (February 3, 2021): 2747–49. http://dx.doi.org/10.1093/bioinformatics/btab079.

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Abstract Summary Genoscapist is a tool to design web interfaces generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome datasets available for Bacillus subtilis and Staphylococcus aureus. Availability and implementation Websites and source code freely accessible at https://genoscapist.migale.inrae.fr

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Sciabola, Simone, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, and Robert V. Stanton. "PFRED: A computational platform for siRNA and antisense oligonucleotides design." PLOS ONE 16, no. 1 (January 22, 2021): e0238753. http://dx.doi.org/10.1371/journal.pone.0238753.

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PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred.

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Bouyssié, David, Jean Lesne, Marie Locard-Paulet, Renaud Albigot, Odile Burlet-Schiltz, and Julien Marcoux. "HDX-Viewer: interactive 3D visualization of hydrogen–deuterium exchange data." Bioinformatics 35, no. 24 (July 9, 2019): 5331–33. http://dx.doi.org/10.1093/bioinformatics/btz550.

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Abstract Summary With the advent of fully automated sample preparation robots for Hydrogen–Deuterium eXchange coupled to Mass Spectrometry (HDX-MS), this method has become paramount for ligand binding or epitope mapping screening, both in academic research and biopharmaceutical industries. However, bridging the gap between commercial HDX-MS software (for raw data interpretation) and molecular viewers (to map experiment results onto a 3D structure for biological interpretation) remains laborious and requires simple but sometimes limiting coding skills. We solved this bottleneck by developing HDX-Viewer, an open-source web-based application that facilitates and quickens HDX-MS data analysis. This user-friendly application automatically incorporates HDX-MS data from a custom template or commercial HDX-MS software in PDB files, and uploads them to an online 3D molecular viewer, thereby facilitating their visualization and biological interpretation. Availability and implementation The HDX-Viewer web application is released under the CeCILL (http://www.cecill.info) and GNU LGPL licenses and can be found at https://masstools.ipbs.fr/hdx-viewer. The source code is available at https://github.com/david-bouyssie/hdx-viewer.

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Abdekhodaie, Ehsan, Javad Hatami, Hadi Bahrami Ehsan, and Reza Kormi-Nouri. "WordCommentsAnalyzer: A windows software tool for qualitative research." F1000Research 7 (September 4, 2018): 536. http://dx.doi.org/10.12688/f1000research.14819.2.

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There is a lack of free software that provides a professional and smooth experience in text editing and markup for qualitative data analysis. Word processing software like Microsoft Word provides a good editing experience, allowing the researcher to effortlessly add comments to text portions. However, organizing the keywords and categories in the comments can become a more difficult task when the amount of data increases. We present WordCommentsAnalyzer, a software tool that is written in C# using .NET Framework and OpenXml, which helps a qualitative researcher to organize codes when using Microsoft Word as the primary text markup software. WordCommentsAnalyzer provides an effective user interface to count codes, to organize codes in a code hierarchy, and to see various data extracts belonging to each code. It also offers basic visualization tools. We illustrate how to use this software by conducting a preliminary content analysis on Tweets with the #successfulaging hashtag. We also demonstrate that the software has satisfactory performance on a large dataset of Iranian journals abstracts. We hope this open-source software will facilitate qualitative data analysis by researchers who are interested in using Word for this purpose.

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Zhuang, Guo Min. "Simulation Environment of Virtual Visualization Technology Based on Apriori Algorithm." Applied Mechanics and Materials 608-609 (October 2014): 1131–35. http://dx.doi.org/10.4028/www.scientific.net/amm.608-609.1131.

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Based on the optimization emergency management legal mechanism of environment emergency, we introduce the Apriori law to the emergencies analysis, and use support degree and confidence degree to improve the Apriori law, so the law has stronger relevance. We use the VC software to programming mathematical model of the law, and use VC source code and engineering design model to design the computer optimization system of environmental emergency management legal mechanism. In order to verify the effectiveness and reliability of the system, we do correlation calculation on legal mechanism before and after optimization, and obtain the correlation visualization process curve of Apriori law, and obtain the optimum structure of environmental emergencies legal mechanism. It provides a new computer method for studying environmental emergency management.

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Baranowski, Mikołaj, Adam Belloum, Marian Bubak, and Maciej Malawski. "Constructing Workflows from Script Applications." Scientific Programming 20, no. 4 (2012): 359–77. http://dx.doi.org/10.1155/2012/683634.

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For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment, which is based on a scripting approach and it extends Ruby language with a high-level API for invoking operations on remote resources. In this paper we describe a tool which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization. We describe how we addressed the issues of analyzing Ruby source code, resolving variable and method dependencies, as well as building workflow representation. The solutions to these problems have been developed and they were evaluated by testing them on complex grid application workflows such as CyberShake, Epigenomics and Montage. Evaluation is enriched by representing typical workflow control flow patterns.

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Dadaev, Tokhir, Daniel A. Leongamornlert, Edward J. Saunders, Rosalind Eeles, and Zsofia Kote-Jarai. "LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations." Bioinformatics 32, no. 6 (November 20, 2015): 949–51. http://dx.doi.org/10.1093/bioinformatics/btv690.

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Abstract Summary: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats. Availability and implementation: LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer. Contact: tokhir.dadaev@icr.ac.uk

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Schultz, Andre, and Rehan Akbani. "SAMMI: a semi-automated tool for the visualization of metabolic networks." Bioinformatics 36, no. 8 (December 18, 2019): 2616–17. http://dx.doi.org/10.1093/bioinformatics/btz927.

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Abstract Summary Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models. Availability and implementation SAMMI has been implemented as a standalone web-based tool and as plug-ins for the COBRA and COBRApy toolboxes. SAMMI and its COBRA plugins are available under the GPL 3.0 license and are available along with documentation, tutorials, and source code at www.SammiTool.com. Supplementary information Supplementary data are available at Bioinformatics online.

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Todorov, Petar V., Benjamin M. Gyori, John A. Bachman, and Peter K. Sorger. "INDRA-IPM: interactive pathway modeling using natural language with automated assembly." Bioinformatics 35, no. 21 (May 9, 2019): 4501–3. http://dx.doi.org/10.1093/bioinformatics/btz289.

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Abstract Summary INDRA-IPM (Interactive Pathway Map) is a web-based pathway map modeling tool that combines natural language processing with automated model assembly and visualization. INDRA-IPM contextualizes models with expression data and exports them to standard formats. Availability and implementation INDRA-IPM is available at: http://pathwaymap.indra.bio. Source code is available at http://github.com/sorgerlab/indra_pathway_map. The underlying web service API is available at http://api.indra.bio:8000. Supplementary information Supplementary data are available at Bioinformatics online.

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Dudek, Christian-Alexander, Carsten Reuse, Regine Fuchs, Janneke Hendriks, Veronique Starck, and Karsten Hiller. "MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification." Bioinformatics 36, no. 12 (April 23, 2020): 3925–26. http://dx.doi.org/10.1093/bioinformatics/btaa251.

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Abstract Summary Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected. Availability and implementation We implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3.

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Georgiou, Georgios, and Simon J. van Heeringen. "fluff: exploratory analysis and visualization of high-throughput sequencing data." PeerJ 4 (July 19, 2016): e2209. http://dx.doi.org/10.7717/peerj.2209.

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Summary.In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available athttp://fluff.readthedocs.org.Availability.fluff is implemented in Python and runs on Linux. The source code is freely available for download athttps://github.com/simonvh/fluff.

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Khalid, Muhammad Farhan, Kanzal Iman, Amna Ghafoor, Mujtaba Saboor, Ahsan Ali, Urwa Muaz, Abdul Rehman Basharat, et al. "PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics." Nucleic Acids Research 49, W1 (May 17, 2021): W510—W515. http://dx.doi.org/10.1093/nar/gkab368.

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Abstract PERCEPTRON is a next-generation freely available web-based proteoform identification and characterization platform for top-down proteomics (TDP). PERCEPTRON search pipeline brings together algorithms for (i) intact protein mass tuning, (ii) de novo sequence tags-based filtering, (iii) characterization of terminal as well as post-translational modifications, (iv) identification of truncated proteoforms, (v) in silico spectral comparison, and (vi) weight-based candidate protein scoring. High-throughput performance is achieved through the execution of optimized code via multiple threads in parallel, on graphics processing units (GPUs) using NVidia Compute Unified Device Architecture (CUDA) framework. An intuitive graphical web interface allows for setting up of search parameters as well as for visualization of results. The accuracy and performance of the tool have been validated on several TDP datasets and against available TDP software. Specifically, results obtained from searching two published TDP datasets demonstrate that PERCEPTRON outperforms all other tools by up to 135% in terms of reported proteins and 10-fold in terms of runtime. In conclusion, the proposed tool significantly enhances the state-of-the-art in TDP search software and is publicly available at https://perceptron.lums.edu.pk. Users can also create in-house deployments of the tool by building code available on the GitHub repository (http://github.com/BIRL/Perceptron).

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Battista, Nicholas A. "Suite-CFD: An Array of Fluid Solvers Written in MATLAB and Python." Fluids 5, no. 1 (February 25, 2020): 28. http://dx.doi.org/10.3390/fluids5010028.

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Computational Fluid Dynamics (CFD) models are being rapidly integrated into applications across all sciences and engineering. CFD harnesses the power of computers to solve the equations of fluid dynamics, which otherwise cannot be solved analytically except for very particular cases. Numerical solutions can be interpreted through traditional quantitative techniques as well as visually through qualitative snapshots of the flow data. As pictures are worth a thousand words, in many cases such visualizations are invaluable for understanding the fluid system. Unfortunately, vast mathematical knowledge is required to develop one’s own CFD software and commercial software options are expensive and thereby may be inaccessible to many potential practitioners. To that extent, CFD materials specifically designed for undergraduate education are limited. Here we provide an open-source repository, which contains numerous popular fluid solvers in 2 D (projection, spectral, and Lattice Boltzmann), with full implementations in both MATLAB and Python3. All output data is saved in the . v t k format, which can be visualized (and analyzed) with open-source visualization tools, such as VisIt or ParaView. Beyond the code, we also provide teaching resources, such as tutorials, flow snapshots, measurements, videos, and slides to streamline use of the software.

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Hübschle, Christian B., George M. Sheldrick, and Birger Dittrich. "ShelXle: a Qt graphical user interface forSHELXL." Journal of Applied Crystallography 44, no. 6 (November 12, 2011): 1281–84. http://dx.doi.org/10.1107/s0021889811043202.

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ShelXleis a graphical user interface forSHELXL[Sheldrick, G. M. (2008).Acta Cryst.A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for theSHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features ofShelXleinclude intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions.ShelXleis completely compatible with all features ofSHELXLand is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

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Chang Liu, Xin Ye, and En Ye. "Source Code Revision History Visualization Tools: Do They Work and What Would it Take to Put Them to Work?" IEEE Access 2 (2014): 404–26. http://dx.doi.org/10.1109/access.2014.2322102.

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WONG, W. ERIC, and JENNY LI. "REDESIGNING LEGACY SYSTEMS INTO THE OBJECT-ORIENTED PARADIGM." International Journal of Software Engineering and Knowledge Engineering 14, no. 03 (June 2004): 255–76. http://dx.doi.org/10.1142/s0218194004001634.

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Object-oriented languages support many modern programming concepts such as information hiding, inheritance, polymorphism, and dynamic binding. As a result, software systems implemented in OO languages are in general more reusable and reliable than others. Many legacy software systems, created before OO programming became popular, need to be redesigned and updated to OO programs. The process of abstracting OO designs from the procedural source code has often been done with limited assistance from program structural diagrams. Most reengineering focuses on the functionality of the original program, and the OO redesign often results in a completely new design based on the designers' understanding of the original program. Such an approach is not sufficient because it may take a significant amount of time and effort for designers to comprehend the original program. This paper presents a computer-aided semi-automatic method that abstracts OO designs from the original procedural source code. More specifically, it is a method for OO redesign based on program structural diagrams, visualization, and execution slices. We conducted a case study by applying this method to an inventory management software system. Results indicate that our method can effectively and efficiently abstract an appropriate OO design out of the original C code. In addition, some of the code from the original system can be automatically identified and reused in the new OO system.

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Li, Kai, Marc Vaudel, Bing Zhang, Yan Ren, and Bo Wen. "PDV: an integrative proteomics data viewer." Bioinformatics 35, no. 7 (August 30, 2018): 1249–51. http://dx.doi.org/10.1093/bioinformatics/bty770.

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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.

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Moore, Ryan M., Amelia O. Harrison, Sean M. McAllister, Shawn W. Polson, and K. Eric Wommack. "Iroki: automatic customization and visualization of phylogenetic trees." PeerJ 8 (February 26, 2020): e8584. http://dx.doi.org/10.7717/peerj.8584.

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Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

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Kaya, Mehmet, and James W. Fawcett. "Identification of Extract Method Refactoring Opportunities through Analysis of Variable Declarations and Uses." International Journal of Software Engineering and Knowledge Engineering 27, no. 01 (February 2017): 49–69. http://dx.doi.org/10.1142/s0218194017500036.

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Software development is a continuous process that usually starts with analyzing the system requirements and proceeds with design, implementation, testing, and maintenance. Regardless of how good an initial design was achieved, quality of source code tends to decay throughout the development process as software evolves. One of the main contributing factors to this degradation of initial quality can be considered as maintenance operations, for instance to enhance performance or other attributes of the system or to fix newly discovered bugs. For such large software systems, development process also requires reusing existing components which may have been implemented by others. Hence, a comprehensible piece of source code, e.g. one that conveys its message about what it is trying to do easily with understandable and modular implementation, significantly reduces time and effort not only for the implementation phase of the development lifecycle; but also for testing and maintenance phases. In other words, while software decay is inevitable, software comprehension plays a determining role in the total cost and effectiveness of both implementation phase and maintenance phase. Therefore, developers should strive to create software components with modular structure and clearer implementation to reduce the development cost. In this paper, we are interested in finding ways to successfully decompose long methods (those with poor initial implementation and/or decayed overtime) into smaller, more comprehensible and readable ones. This decomposition process is known as extract method refactoring and helps to reduce the overall cost of development. Most of the existing refactoring tools require users to select the code fragments that need to be extracted. We introduce a novel technique for this refactoring. This technique seeks refactoring opportunities based on variable declarations and uses confining fully extractable code regions without any user intervention. We implemented this technique as an analysis and visualization tool to help a user identify candidate code fragments to be extracted as separate methods. With this automation tool, developers do not have to manually inspect a foreign code base to select code fragments for refactoring. Through the visual representations we provide, one can observe all suggested refactoring effectively on large scale software systems and decide whether a particular refactoring should be applied. To show the effectiveness of our techniques, we also provide some case studies conducted using this tool and technique both on our own project’s source code and other open-source projects.

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Eskelinen, M. A. "SOFTWARE FRAMEWORK FOR HYPERSPECTRAL DATA EXPLORATION AND PROCESSING IN MATLAB." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-3/W3 (October 19, 2017): 47–50. http://dx.doi.org/10.5194/isprs-archives-xlii-3-w3-47-2017.

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This paper presents a user introduction and a general overview of the MATLAB software package <tt>hsicube</tt> developed by the author for simplifying the data manipulation and visualization tasks often encountered in hyperspectral analysis work, and the design principles and software development methods used by the author. The framework implements methods for slicing, masking, visualization and application of existing functions to hyperspectral data cubes without the need to use explicit indexing or reshaping, as well as enabling expressive syntax for combining these operations on the command line for highly efficient data analysis workflows. It also includes utilities for interfacing with existing file reader scripts for easy access to files using the framework. The <tt>hsicube</tt> framework is released as open source to promote the free use and peer review of the code and enable collaborative development.

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Li, Xuanxuan, Chufeng Li, and Haiguang Liu. "ClickX: a visualization-based program for preprocessing of serial crystallography data." Journal of Applied Crystallography 52, no. 3 (May 28, 2019): 674–82. http://dx.doi.org/10.1107/s1600576719005363.

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Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.

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Potdar, Swapnil, Aleksandr Ianevski, John-Patrick Mpindi, Dmitrii Bychkov, Clément Fiere, Philipp Ianevski, Bhagwan Yadav, et al. "Breeze: an integrated quality control and data analysis application for high-throughput drug screening." Bioinformatics 36, no. 11 (March 2, 2020): 3602–4. http://dx.doi.org/10.1093/bioinformatics/btaa138.

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Abstract Summary High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results. Availability and implementation The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0. Contact swapnil.potdar@helsinki.fi Supplementary information Supplementary data are available at Bioinformatics online.

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Darzi, Youssef, Yuta Yamate, and Takuji Yamada. "FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization." Bioinformatics 35, no. 21 (April 20, 2019): 4519–21. http://dx.doi.org/10.1093/bioinformatics/btz245.

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Abstract Summary Functional annotations and their hierarchical classification are widely used in omics workflows to build novel insight upon existing biological knowledge. Currently, a plethora of tools is available to explore omics datasets at the level of functional annotations, but there is a lack of feature rich and user-friendly tools that help scientists take advantage of their hierarchical classification for additional and often invaluable insights. Here, we present FuncTree2, a user-friendly web application that turns hierarchical classifications into interactive and highly customizable radial trees, and enables researchers to visualize their data simultaneously on all its levels. FuncTree2 features mapping of data from multiple samples and several navigation features like zooming, panning, re-rooting and collapsing of nodes or levels. Availability and implementation FuncTree2 is freely available at https://bioviz.tokyo/functree2/ as a web application and a REST API. Source code is available on GitHub https://github.com/yamada-lab/functree-ng. Supplementary information Supplementary data are available at Bioinformatics online.

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Schaefer, Moritz, Djork-Arné Clevert, Bertram Weiss, and Andreas Steffen. "PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations." Bioinformatics 35, no. 13 (November 16, 2018): 2309–10. http://dx.doi.org/10.1093/bioinformatics/bty935.

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Abstract Summary Single-guide RNAs (sgRNAs) targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state of the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports homology-directed repair template generation for genome editing experiments and the visualization of the mutated amino acids in 3D. Availability and implementation PAVOOC is available under https://pavooc.me and accessible using modern browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend are implemented in Python 3 and ReactJS, respectively. All components run in a simple Docker environment. Supplementary information Supplementary data are available at Bioinformatics online.

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Journal articles on the topic 'Source code visualization'

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