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Smoldyn
Smoldyn is an open-source software application for cell-scale biochemical simulations. It uses particle-based simulation, meaning that it simulates each molecule of interest individually, in order to capture natural stochasticity and yield nanometer-scale spatial resolution. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes in similar manners as in real biochemical systems. History Smoldyn was initially released in 2003 as a simulator that represented chemical reactions between diffusing particles in rectilinear volumes. Further development added support for surfaces, multiscale simulation molecules with excluded volume, rule-based modeling and C/C++ and Python APIs. Smoldyn development has been funded by a postdoctoral NSF grant awarded to Steve Andrews, a US DOE contract awarded to Adam Arkin, a grant from the Computational Research Laboratories (Pune, India) awarded to Upinder Bhalla, a MITRE contract and several NIH grants awarded to Roger B ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Systems Biology Modeling Software
Systems biology relies heavily on building mathematical models 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 unusable, the models developed by that application can be easily transferred to more modern equivalents. This allows scientific research to be reproducible long after the original publication of the work. To obtain more information about a particular tool, click ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Steven S
Stephen or Steven is an English given name, first name. It is particularly significant to Christianity, Christians, as it belonged to Saint Stephen ( ), an early disciple and deacon who, according to the Book of Acts, was stoned to death; he is widely regarded as the first martyr (or "protomartyr") of the Christian Church. The name, in both the forms Stephen and Steven, is often shortened to Steve or Stevie (given name), Stevie. In English, the female version of the name is Stephanie. Many surnames are derived from the first name, including Template:Stephen-surname, Stephens, Stevens, Stephenson, and Stevenson, all of which mean "Stephen's (son)". In modern times the name has sometimes been given with intentionally non-standard spelling, such as Stevan or Stevon. A common variant of the name used in English is Stephan (given name), Stephan ( ); related names that have found some currency or significance in English include Stefan (given name), Stefan (pronounced or in English) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C (programming Language)
C (''pronounced'' '' – like the letter c'') is a general-purpose programming language. It was created in the 1970s by Dennis Ritchie and remains very widely used and influential. By design, C's features cleanly reflect the capabilities of the targeted Central processing unit, CPUs. It has found lasting use in operating systems code (especially in Kernel (operating system), kernels), device drivers, and protocol stacks, but its use in application software has been decreasing. C is commonly used on computer architectures that range from the largest supercomputers to the smallest microcontrollers and embedded systems. A successor to the programming language B (programming language), B, C was originally developed at Bell Labs by Ritchie between 1972 and 1973 to construct utilities running on Unix. It was applied to re-implementing the kernel of the Unix operating system. During the 1980s, C gradually gained popularity. It has become one of the most widely used programming langu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level programming language, high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is type system#DYNAMIC, dynamically type-checked and garbage collection (computer science), garbage-collected. It supports multiple programming paradigms, including structured programming, structured (particularly procedural programming, procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC (programming language), ABC programming language, and he first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000. Python 3.0, released in 2008, was a major revision not completely backward-compatible with earlier versions. Python 2.7.18, released in 2020, was the last release of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, packaged as a Linux distribution (distro), which includes the kernel and supporting system software and library (computing), libraries—most of which are provided by third parties—to create a complete operating system, designed as a clone of Unix and released under the copyleft GPL license. List of Linux distributions, Thousands of Linux distributions exist, many based directly or indirectly on other distributions; popular Linux distributions include Debian, Fedora Linux, Linux Mint, Arch Linux, and Ubuntu, while commercial distributions include Red Hat Enterprise Linux, SUSE Linux Enterprise, and ChromeOS. Linux distributions are frequently used in server platforms. Many Linux distributions use the word "Linux" in their name, but the Free ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MacOS
macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. Within the market of Desktop computer, desktop and laptop computers, it is the Usage share of operating systems#Desktop and laptop computers, second most widely used desktop OS, after Microsoft Windows and ahead of all Linux distributions, including ChromeOS and SteamOS. , the most recent release of macOS is MacOS Sequoia, macOS 15 Sequoia, the 21st major version of macOS. Mac OS X succeeded classic Mac OS, the primary Mac operating systems, Macintosh operating system from 1984 to 2001. Its underlying architecture came from NeXT's NeXTSTEP, as a result of NeXT#1997–2006: Acquisition by Apple, Apple's acquisition of NeXT, which also brought Steve Jobs back to Apple. The first desktop version, Mac OS X 10.0, was released on March 24, 2001. Mac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microsoft Windows
Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sectors of the computing industry – Windows (unqualified) for a consumer or corporate workstation, Windows Server for a Server (computing), server and Windows IoT for an embedded system. Windows is sold as either a consumer retail product or licensed to Original equipment manufacturer, third-party hardware manufacturers who sell products Software bundles, bundled with Windows. The first version of Windows, Windows 1.0, was released on November 20, 1985, as a graphical operating system shell for MS-DOS in response to the growing interest in graphical user interfaces (GUIs). The name "Windows" is a reference to the windowing system in GUIs. The 1990 release of Windows 3.0 catapulted its market success and led to various other product families ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simulation Software
Simulation software is based on the process of modeling a real phenomenon with a set of mathematical formulas. It is, essentially, a program that allows the user to observe an operation through simulation without actually performing that operation. Simulation software is used widely to design equipment so that the final product will be as close to design specs as possible without expensive in process modification. Simulation software with real-time response is often used in gaming, but it also has important industrial applications. When the penalty for improper operation is costly, such as airplane pilots, nuclear power plant operators, or chemical plant operators, a mock up of the actual control panel is connected to a real-time simulation of the physical response, giving valuable training experience without fear of a disastrous outcome. Advanced computer programs can simulate power system behavior, weather conditions, electronic circuits, chemical reactions, mechatronics, heat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU Lesser General Public License
The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate a software component released under the LGPL into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own components. However, any developer who modifies an LGPL-covered component is required to make their modified version available under the same LGPL license. For proprietary software, code under the LGPL is usually used in the form of a shared library, so that there is a clear separation between the proprietary and LGPL components. The LGPL is primarily used for software libraries, although it is also used by some stand-alone applications. The LGPL was developed as a compromise between the strong copyleft of the GNU General Public License (GPL) and more permissive licenses such as the BSD licenses and the MI ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rule-based Modeling
Rule-based modeling is a modeling approach that uses a set of rules that indirectly specifies a mathematical model. The rule-set can either be translated into a model such as Markov chains or differential equations, or be treated using tools that directly work on the rule-set in place of a translated model, as the latter is typically much bigger. Rule-based modeling is especially effective in cases where the rule-set is significantly simpler than the model it implies, meaning that the model is a repeated manifestation of a limited number of patterns. An important domain where this is often the case is biochemical models of living organisms. Groups of mutually corresponding substances are subject to mutually corresponding interactions. BioNetGen is a suite of software tools used to generate mathematical models consisting of ordinary differential equations without generating the equations directly. For example below is an example rule in the BioNetGen format: A(a,a) + B(b) -> A(a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gillespie Algorithm
In probability theory, the Gillespie algorithm (or the Doob–Gillespie algorithm or stochastic simulation algorithm, the SSA) generates a statistically correct trajectory (possible solution) of a stochastic equation system for which the reaction rates are known. It was created by Joseph L. Doob and others (circa 1945), presented by Dan Gillespie in 1976, and popularized in 1977 in a paper where he uses it to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power (see stochastic simulation). As computers have become faster, the algorithm has been used to simulate increasingly complex systems. The algorithm is particularly useful for simulating reactions within cells, where the number of reagents is low and keeping track of every single reaction is computationally feasible. Mathematically, it is a variant of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational system ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systems Biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionist, reductionism) to biological research. This multifaceted research domain necessitates the collaborative efforts of chemists, biologists, mathematicians, physicists, and engineers to decipher the biology of intricate living systems by merging various quantitative molecular measurements with carefully constructed mathematical models. It represents a comprehensive method for comprehending the complex relationships within biological systems. In contrast to conventional biological studies that typically center on isolated elements, systems biology seeks to combine different biological data to create models that illustrate and elucidate the dynamic interactions with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
