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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), modifier ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an application associated with the database. Before digital storage and retrieval of data have become widespread, index cards were used for data storage in a wide range of applications and environments: in the home to record and store recipes, shopping lists, contact information and other organizational data; in business to record presentation notes, project research and notes, and contact information; in schools as flash c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tissue (biology)
In biology, tissue is an assembly of similar cells and their extracellular matrix from the same embryonic origin that together carry out a specific function. Tissues occupy a Biological organisation#Levels, biological organizational level between cell (biology), cells and a complete organ (biology), organ. Accordingly, organs are formed by the functional grouping together of multiple tissues. The English word "tissue" Morphological derivation, derives from the French word "", the past participle of the verb tisser, "to weave". The study of tissues is known as histology or, in connection with disease, as histopathology. Xavier Bichat is considered as the "Father of Histology". Plant histology is Studied Space Shuttle designs, studied in both plant anatomy and Plant physiology, physiology. The classical tools for studying tissues are the Microtome#Applications, paraffin block in which tissue is embedded and then sectioned, the staining, histological stain, and the Microscope, o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache Taverna
Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name ''Taverna Workbench'', then a project under the Apache Software Foundation incubator. Taverna allowed users to integrate many different software components, including web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Data Bank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services was not finite and users could import new service descriptions into the Taverna Workbench. Taverna Workbench provided a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow engine was also available separately, as a Java API, command line tool or as a server. Taverna was used by users in many domains, such as bioinformatics, cheminformatics, medicine, astronomy, social science, music, and digital preservation. ... [...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] |
PubMed
PubMed is an openly accessible, free database which includes primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval. From 1971 to 1997, online access to the MEDLINE database was provided via computer and phone lines primarily through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997. Content In addition to MEDLINE, PubMed provides access to: * older references from the print version of '' Index Medicus'', back to 1951 and earlier * references to some journals before they were indexed in Index Medicus and MEDLINE, for instance ''Science'', '' BMJ'', and ''Annals of Surg ... [...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 SciLab, Octave, BioPAX and RDF/XML. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java applet, in which some networks were presented by following Systems Biolo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MetaCyc
The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. The data have been curated from more than 58,000 publications. MetaCyc has been designed for multiple types of uses. It is often used as an extensive online encyclopedia of metabolism. In addition, MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in the BioCyc Database Collection. MetaCyc is also used in metabolic engineering and metabolomics research. MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. It als ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BRENDA
Brenda is a feminine given name in the English language. Origin The overall accepted origin for the female name Brenda is the Old Nordic male name ''Brandr'' meaning both ''torch'' and ''sword'': evidently the male name Brandr took root in areas of the British Isles under Nordic dominance and through being heard as '"Brenda" was eventually adopted as a female name. The name Brenda was probably influenced by the iconic Gaelic male name Brendan: although linguistically it is unlikely that the name Brendan would yield the name Brenda as its feminine form, the name Brenda is widely considered a feminine form of the name Brendan in Ireland, Scotland, and Wales. History The British Isles Occurring in the medieval legend of Madoc—the purported son of the 12th century historical Welsh ruler Owain Gwynedd by Brenda the daughter of a Viking overlord in Ireland—the name Brenda was apparently until the 19th century confined to the Northern Isles being an evident remnant of the Norther ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reactome
Reactome is a free online database of biological pathways. It is manually curated and authored by PhD-level 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. Reactome is maintained by an international multidisciplinary team from OICR, OHSU, EMBL-EBI and NYULMC, with expertise in pathway curation and annotation, software development, and training and outreach, dedicated to providing the research community with openly accessible biological pathway knowledge. The Reactome project is led by Lincoln Stein (OICR). Peter D'Eustachio (NYULMC), Henning Hermjakob (EMBL-EBI), Guanming Wu (OHSU). 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 num ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Center For Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBank DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pubchem
PubChem is a database of Chemistry, chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains multiple substance descriptions and small molecules with fewer than 100 atoms and 1,000 bonds. More than 80 database vendors contribute to the growing PubChem database. History PubChem was released in 2004 as a component of the Molecular Libraries Program (MLP) of the NIH. As of November 2015, PubChem contains more than 150 million depositor-provided substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results (from over 1 million assay experiments performe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChEBI
Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on "small" chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinformatics Institute (EBI). The term "molecular entity" refers to any "constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity". The molecular entities in question are either products of nature or synthetic products which have potential bioactivity. Molecules directly encoded by the genome, such as nucleic acids, proteins and peptides derived from proteins by proteolytic cleavage, are not as a rule included in ChEBI. ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and nomenclature committee of the International Union of Biochemistry and Molecular Bio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
