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SBML
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. History Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST), Hiroaki Kitano and John C. Doyle assembled a small team of researchers to work on developing better software infrastructure for computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka. Bolouri identified the need for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioModels Database
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 |
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology. This is reflected in its name CellML, although this is simply a name, not an abbreviation. CellML is growing in popularity as a portable description format for computational models, and groups throughout the world are using CellML for modelling or developing software tools based on CellML. CellML is similar to Systems Biology Markup Language SBML but provides greater scope for model modularity and reuse, and is not specific to descriptions of biochemistry. History The CellML language grew from a need to share models of cardiac cell dynamics among researchers at a number of sites across the world. The original working group formed in 1998 consisted of David Bullivant, Warren Hedley, and Poul Nielsen; all t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MIASE
The minimum information about a simulation experiment (MIASE){{cite journal, author1=D. Waltemath , author2=Richard Adams , author3=Daniel A. Beard , author4=rank T. Bergmann , author5=Upinder S. Bhalla , author6=Randall Britten , author7=Vijayalakshmi Chelliah , author8=Michael T. Cooling , author9=Jonathan Cooper , author10=Edmund J. Crampin , author11=Alan Garny , author12=Stefan Hoops , author13=Michael Hucka , author14=Peter Hunter , author15=Edda Klipp , author16=Camille Laibe , author17=Andrew K. Miller , author18=Ion Moraru , author19=David Nickerson , author20=Poul Nielsen , author21=Macha Nikolski , author22=Sven Sahle , author23=Herbert M. Sauro , author24=Henning Schmidt , author25=Jacky L. Snoep , author26=Dominic Tolle , author27=Olaf Wolkenhauer , author28=Nicolas Le Novère , title=Minimum Information About a Simulation Experiment (MIASE). , journal=PLOS Computational Biology , year= 2011 , volume= 7 , issue= 4 , doi=10.1371/journal.pcbi.1001122 , pmid=21552546 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioPAX
BioPAX (Biological Pathway Exchange) is a RDF/ OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are avail ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hiroaki Kitano
is a Japanese scientist. He is the head of th Systems Biology Institute(SBI); President and CEO of Sony Computer Science Laboratories; a Group Director of the Laboratory for Disease Systems Modeling at and RIKEN Center for Integrative Medical Sciences; and a professor at Okinawa Institute of Science and Technology (OIST). Kitano is known for developing AIBO, and the robotic world cup tournament known as Robocup. Education Kitano graduated from International Christian University with a B.A. in physics in 1984. He received a PhD in computer science from Kyoto University in 1991. His PhD thesis in machine translation was titled "Speech-to-speech translation: a massively parallel memory-based approach". His work includes a broad spectrum of publications in artificial intelligence and interactomics. Research From 1988 to 1994, Kitano was a visiting researcher at the Center for Machine Translation at Carnegie Mellon University. At Sony, Kitano started the development of the AIBO r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metabolic Network
A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions. With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human. Several of these networks are available online: Kyoto Encyclopedia of Genes and Genomes (KEGG), EcoCyc, BioCyc and metaTIGER. Metabolic networks are powerful tools for studying and modelling metabolism. Uses Metabolic networks can be used to detect comorbidity patterns in diseased patients. Certain diseases, such as obesity and diabetes, can be present in the same individual concurrently, sometimes one disease being a significant risk factor for the other disease. The disease phenotypes themselves are normally the conse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dynamic Monte Carlo Method
In chemistry, dynamic Monte Carlo (DMC) is a Monte Carlo method for modeling the dynamic behaviors of molecules by comparing the rates of individual steps with random numbers. It is essentially the same as Kinetic Monte Carlo. Unlike the Metropolis Monte Carlo method, which has been employed to study systems at equilibrium, the DMC method is used to investigate non-equilibrium systems such as a reaction, diffusion, and so-forth (Meng and Weinberg 1994). This method is mainly applied to analyze adsorbates' behavior on surfaces. There are several well-known methods for performing DMC simulations, including the First Reaction Method (FRM) and Random Selection Method (RSM). Although the FRM and RSM give the same results from a given model, the computer resources are different depending on the applied system. In the FRM, the reaction whose time is minimum on the event list is advanced. In the event list, the tentative times for all possible reactions are stored. After the select ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Phenomena
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move, grow, and reproduce. Finally, all organisms are able to regulate their own internal environments. Biologists are able to study life at multiple levels of organization, from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations.Based on definition from: Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. Like other scientists, biologists use the scientific met ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MIME
Multipurpose Internet Mail Extensions (MIME) is an Internet standard that extends the format of email messages to support text in character sets other than ASCII, as well as attachments of audio, video, images, and application programs. Message bodies may consist of multiple parts, and header information may be specified in non-ASCII character sets. Email messages with MIME formatting are typically transmitted with standard protocols, such as the Simple Mail Transfer Protocol (SMTP), the Post Office Protocol (POP), and the Internet Message Access Protocol (IMAP). The MIME standard is specified in a series of requests for comments: , , , , and . The integration with SMTP email is specified in and . Although the MIME formalism was designed mainly for SMTP, its content types are also important in other communication protocols. In the HyperText Transfer Protocol (HTTP) for the World Wide Web, servers insert a MIME header field at the beginning of any Web transmission. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
IETF
The Internet Engineering Task Force (IETF) is a standards organization for the Internet and is responsible for the technical standards that make up the Internet protocol suite (TCP/IP). It has no formal membership roster or requirements and all its participants are volunteers. Their work is usually funded by employers or other sponsors. The IETF was initially supported by the federal government of the United States but since 1993 has operated under the auspices of the Internet Society, an international non-profit organization. Organization The IETF is organized into a large number of working groups and birds of a feather informal discussion groups, each dealing with a specific topic. The IETF operates in a bottom-up task creation mode, largely driven by these working groups. Each working group has an appointed chairperson (or sometimes several co-chairs); a charter that describes its focus; and what it is expected to produce, and when. It is open to all who want to partic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MATLAB
MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. Although MATLAB is intended primarily for numeric computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities. An additional package, Simulink, adds graphical multi-domain simulation and model-based design for dynamic and embedded systems. As of 2020, MATLAB has more than 4 million users worldwide. They come from various backgrounds of engineering, science, and economics. History Origins MATLAB was invented by mathematician and computer programmer Cleve Moler. The idea for MATLAB was based on his 1960s PhD thesis. Moler became a math professor at the University of New Mexico an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mathematica
Wolfram Mathematica is a software system with built-in libraries for several areas of technical computing that allow machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other programming languages. It was conceived by Stephen Wolfram, and is developed by Wolfram Research of Champaign, Illinois. The Wolfram Language is the programming language used in ''Mathematica''. Mathematica 1.0 was released on June 23, 1988 in Champaign, Illinois and Santa Clara, California. __TOC__ Notebook interface Wolfram Mathematica (called ''Mathematica'' by some of its users) is split into two parts: the kernel and the front end. The kernel interprets expressions (Wolfram Language code) and returns result expressions, which can then be displayed by the front end. The ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
