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CompuCell3D
CompuCell3D (CC3D) is a three-dimensional C++ and Python software problem solving environment for simulations of biocomplexity problems, integrating multiple mathematical orphogenesismodels. These include the cellular Potts model (CPM) which can model cell clustering, growth, division, death, adhesion, and volume and surface area constraints; as well as partial differential equation solvers for modeling reaction–diffusion of external chemical fields and cell type automata for differentiation. By integrating these models CompuCell3D enables modeling of cellular reactions to external chemical fields such as secretion or resorption, and responses such as chemotaxis and haptotaxis. CompuCell3D is conducive for experimentation and testing biological models by providing a flexible and extensible package, with many different levels of control. High-level steering is possible through CompuCell Player, an interactive GUI built upon Qt threads which execute in parallel with the computat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Systems Biology Modeling Software
Systems biology relies heavily on building mathematical models A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in the natural sciences (such as physics, ... to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers. The following list gives the currently supported software applications available to researchers. The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML, a standard used for representing physiological processes. The advantage of using standard formats is that even though a particular software application may eventually become unsupported and even unusabl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cellular Potts Model
In computational biology, a Cellular Potts model (CPM, also known as the Glazier-Graner-Hogeweg model) is a computational model of cells and tissues. It is used to simulate individual and collective cell behavior, tissue morphogenesis and cancer development. CPM describes cells as deformable objects with a certain volume, that can adhere to each other and to the medium in which they live. The formalism can be extended to include cell behaviours such as cell migration, growth and division, and cell signalling. The first CPM was proposed for the simulation of cell sorting by François Graner and James Glazier as a modification of a large-Q Potts model. CPM was then popularized by Paulien Hogeweg for studying morphogenesis. Although the model was developed to describe biological cells, it can also be used to model individual parts of a biological cell, or even regions of fluid. Model description The CPM consists of a rectangular Euclidean lattice, where each cell is a subset of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Problem Solving Environment
A problem solving environment (PSE) is a completed, integrated and specialised computer software for solving one class of problems, combining automated problem-solving methods with human-oriented tools for guiding the problem resolution. A PSE may also assist users in formulating problem resolution. A PSE may also assist users in formulating problems, selecting algorithm, simulating numerical value and viewing and analysing results. Purpose of PSE Many PSEs were introduced in the 1990s. They use the language of the respective field and often employ modern graphical user interfaces. The goal is to make the software easy to use for specialists in fields other than computer science. PSEs are available for generic problems like data visualization or large systems of equations and for narrow fields of science or engineering like gas turbine design. History The Problem Solving Environment (PSE) released a few years after the release of Fortran and Algol 60. People thought that thi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cellular Differentiation
Cellular differentiation is the process in which a stem cell alters from one type to a differentiated one. Usually, the cell changes to a more specialized type. Differentiation happens multiple times during the development of a multicellular organism as it changes from a simple zygote to a complex system of tissues and cell types. Differentiation continues in adulthood as adult stem cells divide and create fully differentiated daughter cells during tissue repair and during normal cell turnover. Some differentiation occurs in response to antigen exposure. Differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals. These changes are largely due to highly controlled modifications in gene expression and are the study of epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. Although metabolic composition does get altered quite dramaticall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secretion
440px Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical mechanism of cell secretion is via secretory portals at the plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structures embedded in the cell membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell. Secretion in bacterial species means the transport or translocation of effector molecules for example: proteins, enzymes or toxins (such as cholera toxin in pathogenic bacteria e.g. ''Vibrio cholerae'') from across the interior (cytoplasm or cytosol) of a bacterial cell to its exterior. Secretion is a very important mechanism in bacterial functioning and operation in their natural surrounding environment for adaptation and survival. In eukaryotic cells ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Resorption
Resorption is the absorption of cells or tissue into the circulatory system, usually by osteoclasts. Types of resorption include: * Bone resorption * Herniated Disc Resorption * Tooth resorption * Fetal resorption * Blood resorption See also * Nutrient resorption In plants Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plant ..., in plants References Set index articles {{biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemotaxis
Chemotaxis (from '' chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (e.g., glucose) by swimming toward the highest concentration of food molecules, or to flee from poisons (e.g., phenol). In multicellular organisms, chemotaxis is critical to early development (e.g., movement of sperm towards the egg during fertilization) and development (e.g., migration of neurons or lymphocytes) as well as in normal function and health (e.g., migration of leukocytes during injury or infection). In addition, it has been recognized that mechanisms that allow chemotaxis in animals can be subverted during cancer metastasis. The aberrant chemotaxis of leukocytes and lymphocytes also contribute to inflammatory diseases such as atherosclerosis, asthma, and arthr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Haptotaxis
Haptotaxis (from Greek ἅπτω (hapto, "touch, fasten") and τάξις (taxis, "arrangement, order")) is the directional motility or outgrowth of cells, e.g. in the case of axonal outgrowth, usually up a gradient of cellular adhesion sites or substrate-bound chemoattractants (the gradient of the chemoattractant being expressed or bound on a surface, in contrast to the classical model of chemotaxis, in which the gradient develops in a soluble fluid.). These gradients are naturally present in the extracellular matrix (ECM) of the body during processes such as angiogenesis or artificially present in biomaterials where gradients are established by altering the concentration of adhesion sites on a polymer substrate. Clinical Significance Haptotaxis plays a major role in the efficient healing of wounds. For example, when corneal integrity is compromised, epithelial cells quickly cover the damaged area by proliferation and migration (haptotaxis). In the corneal stroma, keratocytes wit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Qt (toolkit)
Qt (pronounced "cute") is cross-platform software for creating graphical user interfaces as well as cross-platform applications that run on various software and hardware platforms such as Linux, Windows, macOS, Android or embedded systems with little or no change in the underlying codebase while still being a native application with native capabilities and speed. Qt is currently being developed by The Qt Company, a publicly listed company, and the Qt Project under open-source governance, involving individual developers and organizations working to advance Qt. Qt is available under both commercial licenses and open-source GPL 2.0, GPL 3.0, and LGPL 3.0 licenses. Purposes and abilities Qt is used for developing graphical user interfaces (GUIs) and multi-platform applications that run on all major desktop platforms and most mobile or embedded platforms. Most GUI programs created with Qt have a native-looking interface, in which case Qt is classified as a '' widget toolki ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Domain-specific Language
A domain-specific language (DSL) is a computer language specialized to a particular application domain. This is in contrast to a general-purpose language (GPL), which is broadly applicable across domains. There are a wide variety of DSLs, ranging from widely used languages for common domains, such as HTML for web pages, down to languages used by only one or a few pieces of software, such as MUSH soft code. DSLs can be further subdivided by the kind of language, and include domain-specific ''markup'' languages, domain-specific ''modeling'' languages (more generally, specification languages), and domain-specific ''programming'' languages. Special-purpose computer languages have always existed in the computer age, but the term "domain-specific language" has become more popular due to the rise of domain-specific modeling. Simpler DSLs, particularly ones used by a single application, are sometimes informally called mini-languages. The line between general-purpose languages and domain ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Design Pattern
A design pattern is the re-usable form of a solution to a design problem. The idea was introduced by the architect Christopher Alexander and has been adapted for various other disciplines, particularly software engineering. The " Gang of Four" book. Details An organized collection of design patterns that relate to a particular field is called a pattern language. This language gives a common terminology for discussing the situations designers are faced with. Documenting a pattern requires explaining why a particular situation causes problems, and how the components of the pattern relate to each other to give the solution. Christopher Alexander describes common design problems as arising from "conflicting forces"—such as the conflict between wanting a room to be sunny and wanting it not to overheat on summer afternoons. A pattern would not tell the designer how many windows to put in the room; instead, it would propose a set of values to guide the designer toward a decisi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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