MolView is an intuitive, Open-Source web-application to make science and education more awesome! MolView is mainly intended as web-based data visualization platform. You can use MolView to search through different scientific databases including compound databases, protein databases and spectral databases, and view records from these databases as interactive visualizations using WebGL and HTML5 technologies. This web application is built on top of the JavaScript libraries and online services listed below. The Virtual Model Kit has been a source of inspiration for the birth of this project.

• JavaScript

• This document provides a briefing on MolView, an open-source web application primarily designed as a web-based data visualization platform for chemistry and related scientific disciplines. The source material highlights its key features, underlying technologies, supported databases, and its context within the Open Educational Resources / Open Source Physics @ Singapore initiative.

  Main Themes and Important Ideas:

  1. Purpose and Target Audience:
  • MolView is presented as an "intuitive, Open-Source web-application to make science and education more awesome!" This emphasizes its dual focus on scientific utility and educational accessibility.
  • The application is listed under "Secondary" and "Junior College," suggesting its primary target audience within the educational system.
  1. Core Functionality: Data Visualization:
  • MolView's main intention is to serve as a "web-based data visualization platform."
  • It enables users to "search through different scientific databases including compound databases, protein databases and spectral databases, and view records from these databases as interactive visualizations using WebGL and HTML5 technologies." This highlights its ability to retrieve and display complex scientific data in an engaging and interactive manner.
  1. Open-Source Nature:
  • The application is explicitly described as "Open-Source," indicating that its source code is freely available and can be modified and distributed. This aligns with the principles of open educational resources.
  1. Underlying Technologies:
  • MolView is built upon a foundation of various JavaScript libraries and online services, including:
  • Ketcher: For reading and writing chemical 2D data. This suggests functionality for drawing and manipulating chemical structures in two dimensions.
  • GLmol v0.47, JSmol, and ChemDoodle Web Components v6.0.1: These are listed as "primary 3D render engine" and "3D render engine and spectrum display," indicating MolView's capability to visualize molecules and potentially spectra in three dimensions.
  • The use of "WebGL and HTML5 technologies" ensures that the application runs within web browsers without the need for additional plugins, enhancing accessibility.
  1. Integration with Scientific Databases:
  • A significant aspect of MolView's functionality is its ability to connect to and retrieve data from a range of prominent scientific databases and REST APIs:
  • NCI/CADD Chemical Identifier Resolver: For identifying and resolving chemical identifiers.
  • RCSB Protein Data Bank (~100.000 macromolecules): Providing access to a vast repository of protein structures.
  • The PubChem Project (~51 million compounds): A comprehensive database of chemical molecules.
  • Crystallography Open Database (~300.000 crystals): Offering structural information on crystalline materials.
  • NIST Chemistry WebBook (~30.000 spectra): Providing access to spectroscopic data.
  • NMR Database: Suggesting access to Nuclear Magnetic Resonance (NMR) data.
  • MyMemory translation API: Potentially for multilingual support or data interpretation.
  • This integration allows users to directly visualize data from these authoritative sources within the MolView interface.
  1. Inspiration from the Virtual Model Kit:
  • The project acknowledges that "The Virtual Model Kit has been a source of inspiration for the birth of this project." This suggests that MolView aims to provide a similar hands-on, visual experience for learning chemistry, but in a web-based and data-driven context.
  1. Context within Open Educational Resources / Open Source Physics @ Singapore:
  • The placement of MolView within this website highlights its role in promoting open access to educational tools and resources in science. The broader context includes a wide array of interactive simulations and applets for physics, mathematics, and other subjects, developed using JavaScript and HTML5. The numerous listed applets and hackathon projects demonstrate an active community focused on creating and sharing interactive educational content.
  1. Licensing and Copyright:
  • MolView v2.4 is copyrighted by Herman Bergwerf and has a license (linked in the source). The content on the Open Educational Resources / Open Source Physics @ Singapore website is licensed under the Creative Commons Attribution-Share Alike 4.0 Singapore License, emphasizing the open and shareable nature of the resources. Commercial use of the EasyJavaScriptSimulations library (mentioned in the broader context) has a separate license.

  Quotes from the Original Source:

  • "MolView is an intuitive, Open-Source web-application to make science and education more awesome!"
  • "MolView is mainly intended as web-based data visualization platform."
  • "You can use MolView to search through different scientific databases including compound databases, protein databases and spectral databases, and view records from these databases as interactive visualizations using WebGL and HTML5 technologies."
  • "The Virtual Model Kit has been a source of inspiration for the birth of this project."

  Conclusion:

  MolView is a valuable open-source web application designed to enhance science and education through interactive data visualization. Its ability to connect with major scientific databases and render chemical and biomolecular structures in 2D and 3D, powered by modern web technologies, makes it a powerful tool for students, educators, and researchers. Its inclusion within the Open Educational Resources / Open Source Physics @ Singapore initiative underscores its commitment to open access and the use of interactive simulations for learning. The wide range of other listed projects on the website indicates a vibrant community focused on developing and sharing similar educational resources.

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  MolView Study Guide

  Overview of MolView

  MolView is an open-source web application designed as a data visualization platform for science and education. It allows users to interactively view records from various scientific databases, including compound, protein, and spectral databases. MolView utilizes WebGL and HTML5 technologies for these visualizations and is built upon several JavaScript libraries and online services. The application aims to make science and education more accessible and engaging through its intuitive interface and interactive features.

  Key Features and Technologies

  • Interactive Visualizations: MolView provides interactive 3D and sometimes 2D visualizations of molecules, proteins, spectra, and crystal structures.
  • Database Integration: It can search and display data from several prominent scientific databases.
  • Open-Source: Being open-source, its code is freely available, allowing for potential modification and contribution by the community.
  • Web-Based: As a web application, it is accessible through any modern web browser without requiring installation.
  • JavaScript Libraries: It relies on specific JavaScript libraries for its functionality, including Ketcher for 2D chemical structure handling and GLmol, JSmol, and ChemDoodle Web Components for 3D rendering.
  • REST APIs: It interfaces with various databases through their REST APIs to retrieve and display data.

  Intended Uses

  • Education: Facilitating the learning and teaching of chemistry, biology, and related sciences through interactive molecular visualization.
  • Research: Providing a tool for researchers to quickly visualize and examine data from various scientific databases.
  • Data Exploration: Allowing users to explore and understand the structures and properties of molecules, proteins, and other scientific entities.

  Quiz

  1. What is the primary purpose of the MolView web application? Describe its main function in 2-3 sentences.
  2. Name two types of scientific databases that users can search and visualize data from using MolView.
  3. What are the two main web technologies that MolView utilizes for its interactive visualizations?
  4. Identify two specific JavaScript libraries mentioned in the text that MolView relies on for its functionality and briefly describe their roles.
  5. What does it mean for MolView to be an "open-source" application, and what are the potential benefits of this?
  6. Explain how MolView accesses and displays information from scientific databases. What kind of interface does it likely use?
  7. Besides compound databases, what other two categories of databases are specifically mentioned as being searchable through MolView?
  8. According to the text, what served as a source of inspiration for the creation of the MolView project?
  9. What is one advantage of MolView being a web-based application compared to a desktop application?
  10. Briefly describe the target audience or main users who would likely benefit from using MolView.

  Quiz Answer Key

  1. The primary purpose of MolView is to serve as a web-based data visualization platform for science and education. It allows users to search and interactively view data, such as molecular structures and spectra, from various scientific databases.
  2. Users can search and visualize data from compound databases (like PubChem) and protein databases (like RCSB Protein Data Bank) using MolView.
  3. The two main web technologies that MolView utilizes for its interactive visualizations are WebGL and HTML5.
  4. Ketcher is a JavaScript library used by MolView for chemical 2D data reading and writing. GLmol (and JSmol and ChemDoodle Web Components) serves as the primary 3D rendering engine for visualizing molecular structures.
  5. Being open-source means that MolView's source code is freely available to the public, allowing users to view, modify, and distribute it. This fosters collaboration, transparency, and the potential for community-driven improvements.
  6. MolView accesses and displays information from scientific databases through their REST APIs (Representational State Transfer Application Programming Interfaces). This allows the web application to request and receive data in a standardized format over the internet.
  7. Besides compound databases, the text specifically mentions protein databases and spectral databases as being searchable through MolView.
  8. The Virtual Model Kit has been a source of inspiration for the birth of the MolView project.
  9. One advantage of MolView being a web-based application is that it can be accessed from any device with a modern web browser and an internet connection, without requiring users to download and install any software.
  10. The target audience for MolView likely includes students and educators in chemistry, biology, and related fields, as well as researchers who need a tool for visualizing molecular and spectral data.

  Essay Format Questions

  1. Discuss the significance of open-source web applications like MolView in the context of science education. How do features like interactive visualization and database integration contribute to a more effective learning experience?
  2. Analyze the role of JavaScript libraries and REST APIs in the functionality of MolView. Explain why these technologies are essential for a modern web-based scientific tool.
  3. Compare and contrast the potential benefits of using MolView for educational purposes versus its utility in scientific research. Consider the different ways each group might interact with the application and its features.
  4. Based on the provided information, evaluate the potential impact of MolView on the accessibility and democratization of scientific data and visualization. Consider its open-source nature and web-based accessibility.
  5. The text mentions several specific databases that MolView can access. Choose two of these databases and discuss the type of information they contain and how a tool like MolView enhances the user's ability to understand and utilize that data.

  Glossary of Key Terms

  • Open-Source: Software for which the original source code is made freely available and may be redistributed and modified.
  • Web Application: A software program that runs on a web server, unlike traditional software programs that run locally on a device's operating system. Users typically access web applications through a web browser.
  • Data Visualization Platform: A tool or system designed to present data in a graphical or visual format to make it easier for humans to understand trends, patterns, and insights.
  • WebGL (Web Graphics Library): A JavaScript API for rendering interactive 3D and 2D graphics within any compatible web browser without the use of plug-ins.
  • HTML5 (Hypertext Markup Language, version 5): The latest evolution of the standard markup language for creating web pages and web applications. It supports multimedia and interactive elements.
  • JavaScript Library: A collection of pre-written JavaScript code that users can utilize to simplify and accelerate the development of web applications by providing reusable functionalities.
  • REST API (Representational State Transfer Application Programming Interface): An architectural style for designing networked applications. RESTful APIs use standard HTTP methods to request and transfer data between systems, often in formats like JSON or XML.
  • Database: A structured collection of data that is organized for easy access, management, and updating. In this context, scientific databases store information about compounds, proteins, spectra, etc.
  • Compound Database: A database that contains information about chemical compounds, including their structures, properties, and identifiers.
  • Protein Database: A database that contains information about proteins, including their amino acid sequences, 3D structures, and functions.
  • Spectral Database: A database that contains spectroscopic data, such as NMR, IR, or mass spectra, which can be used to identify and characterize substances.
  • Interactive Visualization: A visual representation of data that allows users to manipulate and explore the data in real-time, often through features like zooming, rotating, and filtering.
  libraries
  • Ketcher: Chemical 2D data reader/writer
  • GLmol v0.47: primary 3D render engine
  • JSmol: 3D render engine
  • ChemDoodle Web Components v6.0.1: 3D render engine and spectrum display
• Databases/REST API's
  • NCI/CADD Chemical Identifier Resolver
  • RCSB Protein Data Bank (~100.000 macromolecules)
  • The PubChem Project (~51 million compounds)
  • Crystallography Open Database (~300.000 crystals)
  • NIST Chemistry WebBook (~30.000 spectra)
  • NMR Database
  • MyMemory translation API

MolView v2.4  +  Terms of Use
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Credits

Copyright © 2014, 2015 Herman Bergwerf  +  License  +  GitHub

Version:

 https://weelookang.blogspot.com/2020/02/molview-open-source-web-application-for.html