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MIRIAM Registry
The MIRIAM Registry, a by-product of the MIRIAM Guidelines, is a database of namespaces and associated information that is used in the creation of uniform resource identifiers. It contains the set of community-approved namespaces for databases and resources serving, primarily, the biological sciences domain. These shared namespaces, when combined with 'data collection' identifiers, can be used to create globally unique identifiers for knowledge held in data repositories. For more information on the use of URIs to annotate models, see the specification oSBML Level 2 Version 2(and above). A 'data collection' is defined as a set of data which is generated by a provider. A 'resource' is defined as a distributor of that data. Such a description allows numerous resources to be associated with a single collection, allowing accurate representation of how biological information is available on the World Wide Web; often the same information, from a single data collection, may be mirrored by di ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MIRIAM
Miriam ( he, מִרְיָם ''Mīryām'', lit. 'Rebellion') is described in the Hebrew Bible as the daughter of Amram and Jochebed, and the older sister of Moses and Aaron. She was a prophetess and first appears in the Book of Exodus. The Torah refers to her as "Miriam the Prophetess" and the Talmud names her as one of the seven major female prophets of Israel. Scripture describes her alongside of Moses and Aaron as delivering the Jews from exile in Egypt: "For I brought you up out of the land of Egypt and redeemed you from the house of slavery, and I sent before you Moses, Aaron, and Miriam". According to the Midrash, just as Moses led the men out of Egypt and taught them Torah, so too Miriam led the women and taught them Torah. Biblical narrative Miriam was the daughter of Amram and Jochebed; she was the sister of Aaron and Moses, the leader of the Israelites in ancient Egypt. The narrative of Moses' infancy in the Torah describes an unnamed sister of Moses observing him ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Registry Gene Ontology Entry
Registry may refer to: Computing * Container registry, an operating-system-level virtualization registry * Domain name registry, a database of top-level internet domain names * Local Internet registry * Metadata registry, information system for registering metadata * National Internet registry * Regional Internet registry, a database of allocated Internet number resources in a particular region of the world * Windows Registry, a database of configuration settings in Microsoft Windows operating systems * Service List Registry, an audiovisual service discovery platform Gifts * Gift registry, a particular type of wish list, e.g., for anniversaries, birthdays, graduations, honeymoons, housewarmings, showers, weddings ** Bridal registry, a retailers' plan that allows engaged couples to manage the purchase of wedding gifts ** Honeymoon registry, a service that assists engaged and married couples in financing their honeymoons Government and law * A registry is an authoritative list of o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Identifiers
An identifier is a name that identifies (that is, labels the identity of) either a unique object or a unique ''class'' of objects, where the "object" or class may be an idea, physical countable object (or class thereof), or physical noncountable substance (or class thereof). The abbreviation ID often refers to identity, identification (the process of identifying), or an identifier (that is, an instance of identification). An identifier may be a word, number, letter, symbol, or any combination of those. The words, numbers, letters, or symbols may follow an encoding system (wherein letters, digits, words, or symbols ''stand for'' epresentideas or longer names) or they may simply be arbitrary. When an identifier follows an encoding system, it is often referred to as a code or ID code. For instance the ISO/IEC 11179 metadata registry standard defines a code as ''system of valid symbols that substitute for longer values'' in contrast to identifiers without symbolic meaning. Ide ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SourceForge
SourceForge is a web service that offers software consumers a centralized online location to control and manage open-source software projects and research business software. It provides source code repository hosting, bug tracking, mirroring of downloads for load balancing, a wiki for documentation, developer and user mailing lists, user-support forums, user-written reviews and ratings, a news bulletin, micro-blog for publishing project updates, and other features. SourceForge was one of the first to offer this service free of charge to open-source projects. Since 2012, the website has run on Apache Allura software. SourceForge offers free hosting and free access to tools for developers of free and open-source software. , the SourceForge repository claimed to host more than 502,000 projects and had more than 3.7 million registered users. Concept SourceForge is a web-based source code repository. It acts as a centralized location for free and open-source software pr ... [...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 |
Minimum Information Standards
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the wider scientific community. Ultimately, they facilitate the transfer of data from journal articles (unstructured data) into databases (structured data) in a form that enables data to be mined across multiple data sets. Minimal information standards are available for a vast variety of experiment types including microarray (MIAME), RNAseq ( MINSEQE), metabolomics (MSI) and proteomics (MIAPE). Minimum information standards typically have two parts. Firstly, there is a set of reporting requirements – typically presented as a table or a checklist. Secondly, there is a data format. Information about an experiment needs to be converted into the appropriate data format for it to be submitted to the relevant database. In the case of MIAME, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metadata Standards
A metadata standard is a requirement which is intended to establish a common understanding of the meaning or semantics of the data, to ensure correct and proper use and interpretation of the data by its owners and users. To achieve this common understanding, a number of characteristics, or attributes of the data have to be defined, also known as metadata. Metadata Metadata is often defined as ''data about data''. It is “structured information that describes, explains, locates, or otherwise makes it easier to retrieve, use or manage an information resource”, especially in a distributed network environment like for example the internet or an organization.De Carvalho Moura, A.M., Machado Campos, M.L., Barreto, C.M. (1998), A survey on metadata for describing and retrieving Internet resources, World Wide Web, 1, (4), 221-240, Kluwer Academic Publishers A good example of metadata is the cataloging system found in libraries, which records for example the author, title, subject, and lo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Systems Biology
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 gat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
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 th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
