NAMD (Nanoscale Molecular Dynamics) is a molecular dynamics simulation software designed to efficiently simulate the behavior of large biomolecular systems, such as proteins, nucleic acids, and lipid membranes. It is developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign, with the primary goal of studying the dynamics of molecular systems at atomic detail. NAMD is known for its scalability, enabling simulations on both single workstations and large supercomputing clusters.
Neuroscience software refers to a variety of tools and applications designed to analyze, visualize, and interpret data related to the structure and function of the nervous system, including the brain. This software is used by researchers, clinicians, and educators within the fields of neuroscience, psychology, neurology, and related disciplines.
Science software for macOS encompasses a wide range of applications used in scientific research, analysis, modeling, and data visualization. Here are some categories and examples of science software that are commonly used on macOS: ### Data Analysis and Statistics 1. **R and RStudio**: R is powerful software for statistical analysis and data visualization. RStudio is an integrated development environment (IDE) for R.
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.
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.
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.
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.
Quantian is an open-source software project designed for quantitative research and data analysis. It typically provides a suite of tools and libraries for statistical analysis, modeling, and visualization, often integrating various programming languages such as R or Python. Quantian aims to create an environment conducive to quantitative disciplines, making it easier for researchers, data scientists, and analysts to perform their work efficiently.
ScanIP typically refers to a software tool or application that is used for scanning and analyzing IP addresses, networks, or devices. Different tools or services may have variations on this name, but some common functionalities of such tools include: 1. **Network Discovery**: Identifying and mapping devices connected to a network. 2. **Vulnerability Assessment**: Scanning for known vulnerabilities in devices or network configurations. 3. **IP Address Management**: Keeping track of IP address allocations and usage.
SciCast is a forecasting platform that uses crowdsourcing to predict the outcomes of scientific research trends and phenomena. It allows participants to make predictions about various scientific topics, such as technological developments, environmental shifts, and public health issues, among others. Users can create, track, and discuss predictions, engaging with a community of forecasters to refine their insights and analyses. The platform is rooted in the idea that collective intelligence can lead to more accurate predictions than individual assessments.
"Consilience: The Unity of Knowledge" is a book written by the biologist Edward O. Wilson, published in 1998. In this work, Wilson argues for the idea of consilience, which he defines as the principle that evidence from independent, unrelated sources can converge to strong conclusions. The book explores the connections between different fields of knowledge, including science, humanities, and social sciences, advocating for an interdisciplinary approach to understanding the world.
Design science is an interdisciplinary field that focuses on the development and evaluation of artifacts—such as models, frameworks, methods, and systems—that address specific problems in a variety of domains, including information systems, engineering, and the social sciences. The aim of design science is to create innovative solutions that are both practical and theoretically grounded. Key aspects of design science include: 1. **Problem-Solving Focus**: Design science emphasizes solving real-world problems by creating useful artifacts.
XPLOR-NIH is a computational software package used primarily for the analysis of biomolecular structures. It integrates algorithms for the refinement of macromolecular structures, particularly those derived from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. XPLOR-NIH is specifically designed to enhance the interpretation of experimental data and facilitate the modeling of biological macromolecules like proteins and nucleic acids.
"Leviathan and the Air-Pump" is a book written by the philosopher and historian of science Steven Shapin and sociologist Simon Schaffer, published in 1985. The book is a historical and philosophical analysis of the scientific practices and controversies surrounding the experiments of Robert Boyle, particularly his famous air pump experiments in the 17th century.
The term "The Third Culture" was popularized by author and scientist John Brockman in the late 20th century. It refers to a cultural movement where scientists and other intellectuals communicate their complex ideas and discoveries to the general public, bridging the gap between the sciences and the humanities. In this context, the "First Culture" encompasses the traditional literary intellectuals and artists, while the "Second Culture" consists of scientists and researchers.
Antonín Svoboda is a computer scientist known for his contributions to the fields of artificial intelligence, machine learning, and computer vision. Specific details about his work may include research in algorithms, pattern recognition, and possibly contributions to theories or methodologies that enhance computer understanding and processing of visual data. His work may also encompass developments in neural networks, image analysis, or automation processes that leverage machine learning techniques. However, more detailed and up-to-date information can usually be found in academic publications or professional profiles.
Mary Tsingou is known for her contributions to the field of finance, particularly in areas related to financial engineering and risk management. She has been involved in academia and has published research related to financial derivatives and risk assessment.
Evidence-based practice (EBP) is an approach to decision-making in various fields, particularly in healthcare, that emphasizes the use of the best available evidence, combined with clinical expertise and patient values. The goal of EBP is to improve outcomes and enhance the quality of services by integrating the following components: 1. **Best Available Evidence**: This consists of the most current and relevant research findings.
Tobias Preis is a prominent researcher in the field of data science, particularly known for his work involving the application of computational methods and data analytics to understand and model complex systems. He is associated with the University of Warwick in the UK. Preis's research often focuses on using large-scale data sets to analyze trends in human behavior, financial markets, and social phenomena, with an emphasis on how these insights can inform decision-making and strategy.
The level of measurement, also known as the scale of measurement, refers to the relationship between the values of a variable and the mathematical operations that can be performed on those values. Understanding the level of measurement is crucial in statistics and research because it influences the choice of statistical methods and the interpretation of data. There are four primary levels of measurement: 1. **Nominal Level**: This is the most basic level of measurement, where data are categorized without any quantitative value.
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!
Intro to OurBigBook
. Source. We have two killer features:
- 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-calculusArticles 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/derivativeVideo 2. OurBigBook Web topics demo. Source. - 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.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.Figure 4. Visual Studio Code extension tree navigation.Figure 5. Web editor. 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.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. - Infinitely deep tables of contents:
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





