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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 availab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SBPAX
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 availa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virtual Cell
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 spec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systems Biology Ontology
The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling. SBO is part of thBioModels.neteffort. Motivation The rise of Systems Biology, seeking to comprehend biological processes as a whole, highlighted the need to not only develop corresponding quantitative models, but also to create standards allowing their exchange and integration. This concern drove the community to design common data format such as SBML and CellML. SBML is now largely accepted and used in the field. However, as important as the definition of a common syntax is, it is also necessary to make clear the semantics of models. SBO is an attempt to provide the means of annotating models with terms that indicate the intended semantics of an important subset of models in common use in computational systems biology. The development of SBO was first discussed at the 9th SBML Forum Meeting in Heidelberg Oct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WikiPathways
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is built using MediaWiki software, a custom graphical pathway editing tool ( PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems. Pathway content Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and the supported species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, rice and arabidopsis, as well as bacteria and plant species. Using a search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reactome
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is authored by biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format. The website can be used to browse pathways and submit data to a suite of data analysis tools. The underlying data is fully downloadable in a number of standard formats including PDF, SBML and BioPAX. Pathway diagrams use a Systems Biology Graphical Notation (SBGN)-based style. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ConsensusPathDB
The ConsensusPathDB is a molecular functional interaction database, integrating information on protein interactions, genetic interactions signaling, metabolism, gene regulation, and drug-target interactions in humans. ConsensusPathDB currently (release 30) includes such interactions from 32 databases. ConsensusPathDB is freely available for academic use under http://ConsensusPathDB.org. Integrated Databases * Reactome (metabolic and signaling pathways) * KEGG (metabolic pathways only have been integrated in ConsensusPathDB) * HumanCyc (metabolic pathways) * PID - Pathway Interaction Database (signaling pathways) * BioCarta (signaling pathways) * Netpath (signaling pathways) * IntAct (protein interactions) * DIP (protein interactions) * MINT (protein interactions) * HPRD (protein interactions) * BioGRID (protein interactions) * SPIKE (protein interactions, signaling reactions) * WikiPathways (metabolic and signaling pathways) * and many more. Functionalities The Consensus ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NCI-Nature Pathway Interaction Database
The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways.{{cite journal , last=Schaefer, first=Carl F, author2=Anthony Kira , author3=Krupa Shiva , author4=Buchoff Jeffrey , author5=Day Matthew , author6=Hannay Timo , author7=Buetow Kenneth H , date=Jan 2009, title=PID: the Pathway Interaction Database, journal = Nucleic Acids Res., volume=37, issue=Database issue, pages=D674-9, location = England, pmid = 18832364, doi = 10.1093/nar/gkn653, pmc = 2686461 The database contains information about the molecular interactions and reactions that take place in cells, with a particular focus on processes that might be relevant to cancer research and treatment. The database was established as collaboration between the U.S. National Cancer Institute, NIH and Nature Publishing Group in 2005 and was launched in November 2006. In September 2012, active curation was stopped and the PID data are now available in thNetwork Data Exchange, NDEx Da ... [...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 th ... [...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] |
SABIO-Reaction Kinetics Database
SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database storing information about biochemical reactions and their kinetic properties. SABIO-RK comprises a reaction-oriented representation of quantitative information on reaction dynamics based on a given selected publication. This comprises all available kinetic parameters together with their corresponding rate equations, as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined. Additionally, SABIO-RK contains information about the underlying biochemical reactions and pathways including their reaction participants, cellular location and detailed information about the enzymes catalysing the reactions. SABIO-RK Database Content The data stored in SABIO-RK in a comprehensive manner is mainly extracted manually from literature. This includes reactions, their participants (substrates, products), modifiers ( ... [...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] |