Abalone is a molecular mechanics program specifically designed for the simulation of molecular systems. It is part of the broader category of computational chemistry tools that are used to study the physical and chemical properties of molecules and materials. Molecular mechanics involves the use of classical physics principles to model molecular systems, focusing on the positions of atoms, the forces acting between them, and the potential energy of the entire system.
Advanced Chemistry Development, Inc. (ACD) is a company that specializes in software and solutions for researchers and scientists in the fields of chemistry and related disciplines. Founded in 1994, ACD focuses on providing tools for chemical data management, analysis, and visualization. Their software products are used for various applications, including: 1. **Chemical Information Management**: Tools for organizing and storing chemical data, which can help streamline research processes and improve data accessibility.
Automated Data Inquiry for Oil Spills refers to the use of technology, such as software and algorithms, to monitor, analyze, and respond to oil spill incidents in an efficient and effective manner. This approach leverages data collection, processing, and analysis to provide real-time insights about spills, including their location, size, spread, and potential environmental impacts.
Avizo is a software application used for visualization and analysis of scientific and industrial data, particularly in the fields of materials science, life sciences, and engineering. Developed by FEI (now part of Thermo Fisher Scientific), Avizo provides a powerful platform for researchers and engineers to process, analyze, and visualize complex three-dimensional (3D) data obtained from various sources, including microscopy, tomography, and simulations.
The Climate and Forecast (CF) Metadata Conventions are a set of guidelines and best practices developed to enhance the representation and exchange of climate and forecast data in a standardized manner. These conventions are particularly useful for ensuring that datasets are well-described and easily interpretable, facilitating the sharing and utilization of climate data among researchers, modelers, and policymakers.
Molecular mechanics modeling is a computational technique used to simulate the physical movements of atoms and molecules. Various software packages specialize in molecular mechanics, each offering unique features, capabilities, and user experiences. Here’s a comparison of some popular software for molecular mechanics modeling, focusing on their key aspects: ### 1. **CHARMM (Chemistry at HARvard Macromolecular Mechanics)** - **Type**: Open-source with commercial support (CHARMM-GUI).
CrysTBox, often stylized as "CrysTBox," is a cloud-based file storage and collaboration platform that allows users to store, manage, and share files securely. It offers various features typical of cloud storage solutions, including file versioning, access control, collaborative tools, and integrations with third-party applications. CrysTBox aims to provide a user-friendly interface for both personal and professional use, enabling efficient file management and collaboration.
Discovery Studio is a software suite developed by BIOVIA, a part of Dassault Systèmes, that is used for scientific research and development in the fields of chemistry, biology, and materials science. It provides tools for modeling, simulation, and visualization of molecular structures and interactions, which are useful in various applications such as drug discovery, materials design, and bioinformatics.
The Earth System Grid (ESG) is a collaborative framework and infrastructure designed to facilitate the sharing and accessibility of large geospatial datasets and model output related to the Earth's climate and environmental systems. It aims to support research in climate science, Earth system science, and related fields by providing a platform for data discovery, access, and sharing.
An Electronic Lab Notebook (ELN) is a digital version of a traditional laboratory notebook used by researchers, scientists, and engineers to document their experiments, research findings, and other scientific activities. ELNs are designed to provide a more efficient, organized, and accessible way to collect data, while enhancing collaboration and compliance with regulatory requirements.
Gene Relationships Across Implicated Loci (GRAIL) is a computational biology concept and tool used to identify and analyze genes that may be associated with certain biological phenomena, such as diseases or traits, based on genetic loci that have been implicated in those conditions. The approach typically involves the integration of various types of genomic data, including genome-wide association studies (GWAS) results, gene expression data, and biological pathway information.
IMOD is a software package primarily used for the three-dimensional visualization and analysis of electron microscopy data. It is particularly tailored for working with high-resolution images acquired through electron tomography and provides tools for visualizing, reconstructing, and analyzing 3D structures at the nanoscale. IMOD is widely utilized in various scientific fields, especially in biology and materials science, where researchers study cellular structures, proteins, and other intricate nanoscale features.
Insilico Medicine is a biotechnology company that focuses on artificial intelligence and machine learning to accelerate drug discovery and development. Founded in 2014, Insilico combines advanced computational methods with biology to identify new drug candidates and predict their potential efficacy and safety. The company's work includes the use of generative models for drug design, biomarker discovery, and the exploration of age-related diseases and other conditions.
JUICE (Java and Universal Interface for Computational Environments) is an open-source software toolkit aimed at providing a framework for scientific computing and data analysis, particularly for the fields of physics and engineering. It is designed to facilitate the development and execution of simulations, models, and data processing workflows. The software typically includes a wide variety of features such as: 1. **Modularity**: JUICE supports the integration of different modules, allowing users to combine various computational tools and libraries.
KStars is a free, open-source astronomy software application that provides a virtual desktop planetarium. It was developed primarily for Linux, though it is also available for other operating systems such as Windows and macOS. KStars allows users to simulate the night sky from any location on Earth at any date and time.
Laboratory informatics refers to the collection, management, integration, and analysis of data generated in laboratory settings. This field encompasses various technologies, tools, and processes designed to improve the efficiency, accuracy, and reproducibility of laboratory operations and research. Key components of laboratory informatics include: 1. **Data Management**: Organizing and storing experimental data, protocols, and results to ensure easy access, retrieval, and analysis.
Systems biology modeling software encompasses a variety of tools designed to simulate and analyze biological systems at various scales, from molecular and cellular levels to whole organisms. Here is a list of notable systems biology modeling software: 1. **CellDesigner** - A graphical modeling tool for biochemical networks, supporting systems biology markup language (SBML). 2. **COPASI** - A software application for modeling and simulating biochemical networks, offering a user-friendly interface to define models using ordinary differential equations.
Maxim DL is a software program widely used in the field of astrophotography and astronomy. Developed by Diffraction Limited, it provides a range of tools and features for capturing, processing, and analyzing astronomical images. Some of its key functionalities include: 1. **Image Acquisition**: Maxim DL supports various telescopes and cameras, allowing users to control these devices for capturing images of celestial objects.
MeVisLab is a software platform designed for medical image processing and visualization. It provides a comprehensive environment for the development, integration, and deployment of imaging algorithms and applications, primarily focusing on various aspects of medical imaging such as CT, MRI, and ultrasound data. Key features of MeVisLab include: 1. **Modular Architecture**: MeVisLab uses a node-based architecture, allowing users to create complex image processing workflows by connecting various functional modules (nodes) without the need for extensive programming.
Tomviz is an open-source software platform designed for visualizing and analyzing scientific data, particularly in the field of electron microscopy and three-dimensional (3D) imaging. It provides tools for reconstructing 3D volumes from 2D image datasets, enabling researchers to explore and interpret complex datasets more effectively. The software is commonly used in various scientific fields, including materials science, biology, and medical imaging.

Pinned article: Introduction to the OurBigBook Project

Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
We have two killer features:
  1. topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculus
    Articles of different users are sorted by upvote within each article page. This feature is a bit like:
    • a Wikipedia where each user can have their own version of each article
    • a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
    This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
    Figure 1.
    Screenshot of the "Derivative" topic page
    . View it live at: ourbigbook.com/go/topic/derivative
  2. local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:
    This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
    Figure 5. . You can also edit articles on the Web editor without installing anything locally.
    Video 3.
    Edit locally and publish demo
    . Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.
  3. https://raw.githubusercontent.com/ourbigbook/ourbigbook-media/master/feature/x/hilbert-space-arrow.png
  4. Infinitely deep tables of contents:
    Figure 6.
    Dynamic article tree with infinitely deep table of contents
    .
    Descendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact