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Modelling Biological Systems
Modelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes. An unexpected emergent property of a complex system may be a result of the interplay of the cause-and-effect among simpler, integrated parts (see biological organisation). Biological systems manifest many important examples of emergent properties in the complex interplay of components. Traditional study of biological systems requires reductive methods in which quantities of data are gathered ... [...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. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent property, emergent properties, properties of cell (biology), cells, tissue (biology), tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioModels
BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in peer-reviewed scientific literature. The models stored in BioModels' curated branch are compliant with MIRIAM, the standard of model curation and annotation. The models have been simulated by curators to check that when run in simulations, they provide the same results as described in the publication. Model components are annotated, so the users can conveniently identify each model element and retrieve further information from other resources. Modellers can submit the models in SBML and CellML. Models can subsequently be downloaded in SBMLVCML |
OpenWorm
OpenWorm is an international open science project for the purpose of simulating the roundworm ''Caenorhabditis elegans'' at the cellular level. Although the long-term goal is to model all 959 cells of the ''C. elegans'', the first stage is to model the worm's locomotion by simulating the 302 neurons and 95 muscle cells. This bottom up simulation is being pursued by the OpenWorm community. As of 2014, a physics engine called Sibernetic has been built for the project and models of the neural connectome and a muscle cell have been created in NeuroML format. A 3D model of the worm anatomy can be accessed through the web via the OpenWorm browser. The OpenWorm project is also contributing to develop Geppetto, a web-based multi-algorithm, multi-scale simulation platform engineered to support the simulation of the whole organism. __TOC__ Background: ''C. elegans'' The roundworm ''Caenorhabditis elegans'' is a free-living, transparent nematode, about 1 mm in length, that live ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell Membrane
The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment (the extracellular space). The cell membrane consists of a lipid bilayer, made up of two layers of phospholipids with cholesterols (a lipid component) interspersed between them, maintaining appropriate membrane fluidity at various temperatures. The membrane also contains membrane proteins, including integral proteins that span the membrane and serve as membrane transporters, and peripheral proteins that loosely attach to the outer (peripheral) side of the cell membrane, acting as enzymes to facilitate interaction with the cell's environment. Glycolipids embedded in the outer lipid layer serve a similar purpose. The cell membrane controls the movement of substances in and out of cells and organelles, being selectively permeable to ions a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Membrane Computing
Membrane computing (or MC) is an area within computer science that seeks to discover new computational models from the study of biological cells, particularly of the cellular membranes. It is a sub-task of creating a cellular model. Membrane computing deals with distributed and parallel computing models, processing multisets of symbol objects in a localized manner. Thus, evolution rules allow for evolving objects to be encapsulated into compartments defined by membranes. The communications between compartments and with the environment play an essential role in the processes. The various types of membrane systems are known as P systems after Gheorghe Păun who first conceived the model in 1998. An essential ingredient of a P system is its membrane structure, which can be a hierarchical arrangement of membranes, as in a cell, or a net of membranes (placed in the nodes of a graph), as in a tissue or a neural net. P systems are often depicted graphically with drawings. The intui ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mycoplasma Genitalium
''Mycoplasma genitalium'' (''MG'', commonly known as Mgen) is a sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans. Medical reports published in 2007 and 2015 state that Mgen is becoming increasingly common. Resistance to multiple antibiotics is becoming prevalent, including to azithromycin, which until recently was the most reliable treatment. The bacteria was first isolated from the urogenital tract of humans in 1981, and was eventually identified as a new species of ''Mycoplasma'' in 1983. It can cause negative health effects in men and women. It also increases the risk factor for HIV spread with higher occurrences in those previously treated with the azithromycin antibiotics. Specifically, it causes urethritis in both men and women, and also cervicitis and pelvic inflammation in women. It presents clinically similar symptoms to that of ''Chlamydia trachomatis'' infection and has shown hi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Science Foundation
The National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health. With an annual budget of about $8.3 billion (fiscal year 2020), the NSF funds approximately 25% of all federally supported basic research conducted by the United States' colleges and universities. In some fields, such as mathematics, computer science, economics, and the social sciences, the NSF is the major source of federal backing. The NSF's director and deputy director are appointed by the President of the United States and confirmed by the United States Senate, whereas the 24 president-appointed members of the National Science Board (NSB) do not require Senate confirmation. The director and deputy director are responsible for administration, planning, budgeting and day-to-day operations of the foundation, while t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Predictive Modelling
Predictive modelling uses statistics to predict outcomes. Most often the event one wants to predict is in the future, but predictive modelling can be applied to any type of unknown event, regardless of when it occurred. For example, predictive models are often used to detect crimes and identify suspects, after the crime has taken place. In many cases the model is chosen on the basis of detection theory to try to guess the probability of an outcome given a set amount of input data, for example given an email determining how likely that it is spam. Models can use one or more classifiers in trying to determine the probability of a set of data belonging to another set. For example, a model might be used to determine whether an email is spam or "ham" (non-spam). Depending on definitional boundaries, predictive modelling is synonymous with, or largely overlapping with, the field of machine learning, as it is more commonly referred to in academic or research and development contexts. W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Translation (biology)
In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription (biology), transcription of DNA to RNA in the cell's nucleus (cell), nucleus. The entire process is called gene expression. In translation, mRNA, messenger RNA (mRNA) is decoded in a ribosome, outside the nucleus, to produce a specific amino acid chain, or polypeptide. The polypeptide later protein folding, folds into an Activation energy, active protein and performs its functions in the Cell (biology), cell. The ribosome facilitates decoding by inducing the binding of Base pair, complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome. Translation proceeds in three phases: # Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcription (biology)
Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). mRNA comprises only 1–3% of total RNA samples. Less than 2% of the human genome can be transcribed into mRNA ( Human genome#Coding vs. noncoding DNA), while at least 80% of mammalian genomic DNA can be actively transcribed (in one or more types of cells), with the majority of this 80% considered to be ncRNA. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the following general steps: # RNA polymerase, together with one or more general transcription factors, binds to promoter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lotka Volterra Dynamics
Alfred James Lotka (March 2, 1880 – December 5, 1949) was a US mathematician, physical chemist, and statistician, famous for his work in population dynamics and energetics. An American biophysicist, Lotka is best known for his proposal of the predator–prey model, developed simultaneously but independently of Vito Volterra. The Lotka–Volterra model is still the basis of many models used in the analysis of population dynamics in ecology. Life Lotka was born in Lwów, Austria-Hungary (now in Ukraine) to Polish-American parents. His parents, Jacques and Marie (Doebely) Lotka, were US nationals. He gained his B.Sc. in 1901 at the University of Birmingham, England, he did graduate work in 1901–02 at Leipzig University, received an M.A. in 1909 at Cornell University and a D. Sc. at Birmingham University in 1912. ;Occupations * Assistant chemist for General Chemical Company (1902–1908, 1914–1919) * Patent examiner for US Patent Office (1909) * Assistant physicist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
