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List Of Systems Biology Modelling 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, cli ... [...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] |
BSD-3
BSD licenses are a family of permissive free software licenses, imposing minimal restrictions on the use and distribution of covered software. This is in contrast to copyleft licenses, which have share-alike requirements. The original BSD license was used for its namesake, the Berkeley Software Distribution (BSD), a Unix-like operating system. The original version has since been revised, and its descendants are referred to as modified BSD licenses. BSD is both a license and a class of license (generally referred to as BSD-like). The modified BSD license (in wide use today) is very similar to the license originally used for the BSD version of Unix. The BSD license is a simple license that merely requires that all code retain the BSD license notice if redistributed in source code format, or reproduce the notice if redistributed in binary format. The BSD license (unlike some other licenses e.g. GPL) does not require that source code be distributed at all. Terms In addition to t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lists Of Software
The following outline is provided as an overview of and topical guide to software: Software – collection of computer programs and related data that provides the information for the functioning of a computer. It is held in various forms of memory of the computer. It comprises procedures, algorithms, and documentation concerned with the operation of a data processing system. The term was coined to contrast to the term hardware, meaning physical devices. In contrast to hardware, software "cannot be touched". Software is also sometimes used in a more narrow sense, meaning application software only. Sometimes the term includes data that has not traditionally been associated with computers, such as film, tapes, and records. Types * Application software – end-user applications of computers such as word processors or video games, and ERP software for groups of users. ** Business software ** Computer-aided design ** Databases ** Decision-making software ** Educational software ** ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
{{short description, none The list of bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ... software tools can be split up according to the license used: * List of proprietary bioinformatics software * List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software ** List of sequence alignment software ** List of alignment visualization software ** Alignment-free sequence analysis ** De novo sequence assemblers ** List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools ** List of phylogenetics software ** List of phylogenetic tree visualization software ** :Metagenomics_software *S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metabolic Control Analysis
In biochemistry, metabolic control analysis (MCA) is a mathematical framework for describing Metabolic pathway, metabolic, Cell signaling#Signaling pathways, signaling, and genetic pathways. MCA quantifies how variables, such as fluxes and Chemical species, species concentrations, depend on Network (mathematics), network parameters. In particular, it is able to describe how network-dependent properties, called control coefficients, depend on Local property, local properties called Elasticity of a function, elasticities or elasticity coefficients. MCA was originally developed to describe the control in metabolic pathways but was subsequently extended to describe signaling and Gene regulatory network, genetic networks. MCA has sometimes also been referred to as ''Metabolic Control Theory,'' but this terminology was rather strongly opposed by Henrik Kacser, one of the founders. More recent work has shown that MCA can be Isomorphism, mapped directly on to classical control theory an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
English Electric KDF9
KDF9 was an early British 48-bit computer designed and built by English Electric (which in 1968 was merged into International Computers Limited (ICL)). The first machine came into service in 1964 and the last of 29 machines was decommissioned in 1980 at the National Physical Laboratory. The KDF9 was designed for, and used almost entirely in, the mathematical and scientific processing fields in 1967, nine were in use in UK universities and technical colleges. The KDF8, developed in parallel, was aimed at commercial processing workloads. The KDF9 was an early example of a machine that directly supported multiprogramming, using offsets into its core memory to separate the programs into distinct virtual address spaces. Several operating systems were developed for the platform, including some that provided fully interactive use through PDP-8 machines acting as smart terminal servers. A number of compilers were available, notably both checkout and globally optimizing compilers for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maxima (software)
Maxima () is a software package for performing computer algebra calculations in mathematics and the physical sciences. It is written in Common Lisp and runs on all POSIX platforms such as macOS, Unix, BSD, and Linux, as well as under Microsoft Windows and Android. It is free software released under the terms of the GNU General Public License (GPL). History Maxima is based on a 1982 version of Macsyma, which was developed at MIT with funding from the United States Department of Energy and other government agencies. A version of Macsyma was maintained by Bill Schelter from 1982 until his death in 2001. In 1998, Schelter obtained permission from the Department of Energy to release his version under the GPL. That version, now called Maxima, is maintained by an independent group of users and developers. Maxima does not include any of the many modifications and enhancements made to the commercial version of Macsyma during 1982–1999. Though the core functionality remains similar, co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
VCell
Virtual Cell (VCell) is an open-source software platform for modeling and simulation of living organisms, primarily cells. It has been designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. Concept Virtual Cell is an advanced software platform for modeling and simulating reaction kinetics, membrane transport and diffusion in the complex geometries of cells and multicellular tissues. VCell models have a hierarchical tree structure. The trunk level is the "Physiology" consisting of compartments, species and chemical reactions, and reaction rates that are functions of concentrations. Given initial concentrations of species, VCell can calculate how these concentrations change over time. How these numerical simulations are performed, is determined through a number of "Applications", which specify whether simulations will be deterministic or stochastic, and spatial or compartmental; multiple "Applications" can also specify ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
LGPL
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 th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GPL 3
The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first copyleft license available for general use. It was originally written by Richard Stallman, the founder of the Free Software Foundation (FSF), for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. The licenses in the GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. The GPL is more restrictive than the GNU Lesser General Public License, and even more distinct from the more widely used permissive software licenses such as BSD, MIT, and Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open-source software (FOSS) domain. Promine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
