Phytosociology is a branch of ecology that studies the composition, structure, and distribution of plant communities, as well as the relationships among different plant species within these communities. It focuses on understanding how various environmental factors, such as soil type, climate, and topography, influence the distribution and abundance of plant species, and how these species interact with one another and with their ecosystems.
The term "relict" can refer to different concepts depending on the context in which it is used: 1. **Biology and Ecology**: In biological terms, a "relict" often refers to a species or population that has survived or persisted from an earlier geological period or environmental condition. These species are typically found in isolated areas and can provide insight into historical biodiversity.
Biological sequence format refers to the standardized ways of representing biological sequences, such as DNA, RNA, or protein sequences, in a textual format that can be easily read, shared, and analyzed by computational tools and biologists. Different formats serve various purposes and can include information about the sequence, annotations, and metadata. Some common biological sequence formats include: 1. **FASTA Format**: This is one of the most widely used formats for representing nucleotide or protein sequences.
Bioinformatics and computational biology are interdisciplinary fields that combine biology, computer science, and mathematics to analyze and interpret biological data. Journals in this area publish research articles, reviews, and methodologies that advance our understanding and application of these fields. ### Bioinformatics: Bioinformatics primarily focuses on the development and application of computational tools and techniques for managing and analyzing biological data. This often involves sequence analysis, genomics, proteomics, systems biology, and data mining in biological research.
"Omics" is a term that encompasses a variety of fields of study that involve analyzing biological molecules on a large scale. It is derived from the suffix "-ome," which denotes a comprehensive collection or system. The most common omics disciplines include: 1. **Genomics**: The study of the genome, which is the complete set of DNA within an organism, including its genes and non-coding sequences.
Phylogenetics is a field of biology that studies the evolutionary relationships among various biological species or entities based on their physical and genetic characteristics. This discipline primarily uses the concept of a phylogenetic tree, a diagram that represents the evolutionary pathways and relationships among different organisms, showing how they diverged from common ancestors over time.
A Backbone-dependent rotamer library is a collection of pre-computed side-chain conformations (rotamers) for amino acids that take into account the influence of the protein backbone on the orientation and flexibility of the side chains. In protein structures, the side-chain conformation of amino acids can be significantly affected by their environment, particularly by the dihedral angles of the backbone.
Biological data refers to any data that is derived from biological systems, organisms, or processes. It encompasses a wide range of information related to the structure, function, and interactions of biological molecules, cells, tissues, organisms, and ecosystems. This type of data can be collected from various sources and can be used for a multitude of research and application purposes, including genomics, proteomics, ecology, medicine, and more.
Consed is a software application used primarily for the editing and visualization of DNA sequence data, particularly in the context of genome assembly and analysis. It is designed to assist researchers in reviewing and refining sequence assemblies by providing tools for displaying sequence alignments, viewing quality scores, and facilitating the identification of errors or gaps in the sequence data.
CASP can refer to several things, depending on the context. Below are a few of the most common meanings: 1. **Certified Advanced Security Practitioner (CASP)**: In the field of information technology, CASP is a certification offered by CompTIA. It is designed for advanced IT professionals who want to demonstrate their skills in enterprise security, risk management, and advanced security solutions.
Critical Assessment of Function Annotation (CAFA) is an evaluation initiative designed to assess the accuracy and effectiveness of computational methods for predicting the function of proteins. Established in 2010, CAFA serves as a benchmark for evaluating how well computational models can predict biological functions based on sequence or structural data. The main aspects of CAFA include: 1. **Data Input**: The initiative uses a large set of proteins with well-characterized functions.
A Chip Description File (CDF) is a critical component in semiconductor design and fabrication. It generally serves as a file that contains the descriptions of the characteristics of a chip or integrated circuit (IC) design. Here are key aspects related to Chip Description Files: 1. **Standardization**: CDFs help standardize how chip parameters and features are described, making it easier for designers, engineers, and manufacturing teams to understand the specifications of a given chip.
Computational genomics is a field of study that combines computer science, statistics, mathematics, and biology to analyze and interpret genomic data. It involves the development and application of algorithms, software tools, and models to understand the structure, function, evolution, and regulation of genomes. Key aspects of computational genomics include: 1. **Data Analysis**: Processing and analyzing large-scale genomic data generated by high-throughput sequencing technologies. This includes DNA, RNA, and epigenomic data.
HubMed is a specialized search engine designed for accessing and searching the medical literature, primarily focused on biomedical and life sciences. It was created to provide more refined search capabilities compared to general search engines and even some traditional databases. Users can search for articles, abstracts, and other resources from a variety of medical journals and publications. The platform allows users to customize their searches using features like filters, tags, and personalized collections, making it easier to find relevant research content quickly.
Fluxomics is a sub-discipline of metabolomics that focuses on studying the rates of metabolic reactions within a biological system. It aims to measure and analyze the flow of metabolites through various metabolic pathways to understand how cells and organisms produce and utilize energy and biomass. By examining fluxes rather than just the concentrations of metabolites, fluxomics provides insights into metabolic dynamics, regulation, and interactions among metabolic pathways.
GC skew is a metric used to analyze the relative abundance of guanine (G) and cytosine (C) nucleotides in a segment of DNA. It is calculated to identify regions of DNA that may differ in their GC content, which can have implications for understanding genomic features, such as replication origins, gene density, and overall genomic stability.
Hierarchical Editing Language for Macromolecules (HELIX) is a specialized language designed for representing and manipulating macromolecular structures, often used in computational biology and bioinformatics. The primary purpose of HELIX is to provide a means to describe complex biological macromolecules, such as proteins and nucleic acids, in a structured and hierarchical format.
The Human Genome Project (HGP) was a landmark scientific endeavor that aimed to map and understand all the genes of the human species. It was officially launched in 1990 and completed in April 2003, although the analysis of the data continued for some time afterward. The primary goals of the HGP included: 1. **Sequencing the Human Genome**: Determining the complete sequence of the human DNA, which consists of approximately 3 billion base pairs.
As of my last update, "Infologs" could refer to various concepts or brands, depending on the context. However, it's often associated with data management, information logging, or analytics platforms that help organizations manage and analyze their data more effectively.
Here is a list of some prominent bioinformatics journals where researchers publish their findings related to the field: 1. **Bioinformatics** - A leading journal in the field, covering algorithms, computational methods, and software tools for analyzing biological data. 2. **BMC Bioinformatics** - An open-access journal that publishes research on algorithms, software, and techniques used in bioinformatics.

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 2.
    You can publish local OurBigBook lightweight markup files to either https://OurBigBook.com or as a static website
    .
    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.
  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