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Proteomics Identifications Database
The PRIDE (PRoteomics IDEntifications database) is a public data repository of mass spectrometry-based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team. Originally designed by Lennart Martens in 2003 during a stay at the European Bioinformatics Institute as a Marie Curie fellow of the European Commission in the "Quality of Life" Programme (Contract number: QLRI-1999-50595), PRIDE was established as a production service in 2005. The original grant application document from June 2013 to start construction of PRIDE has since been published in a viewpoint article. Several similar proteomics databases have been built, including the GPMDB, PeptideAtlas, Proteinpedia and the NCBI Peptidome. The PRIDE database constitutes a structured data repository, and stores the original experimental data from the researchers without editorial control over the submitted data. In total, PRIDE contains data from about 60 species, the biggest f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionization, ionized, for example by bombarding it with a Electron ionization, beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragmen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefited greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity, and is an important component of function ... [...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. Further, 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-based and not so. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including Ensembl (housing whole genome sequence data), UniProt (protein sequence and annotation database) and Protein Data Bank (protein and nucleic acid tertiary structure database). A variety of online services and tools is provided, such as Basic Local Alignment Search Tool (BLAST) or Clust ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Marie Curie Actions
Marie may refer to the following. People Given name * Marie (given name), including a list of people and fictional characters with the name ** List of people named Marie * Marie (Japanese given name) Surname * Jean Gabriel-Marie, French composer * Jean Gabriel Marie (1907–1970), his son, French romantic composer Arts, entertainment and media Film, television and stage * ''Marie'' (1980 TV series), an American television show * ''Marie'' (1985 film), an American biography of Marie Ragghianti * ''Marie'' (2020 film), a documentary short about homebirths * ''Marie'' (talk show), hosted by Marie Osmond * ''Marie'' (TV pilot), a 1979 American pilot with Marie Osmond * ''Marie'', a 2009 ballet by Stanton Welch Literature * ''Marie'' (novel), by H. Rider Haggard, 1912 Music * ''Marie'', a 2008 EP by the Romance of Young Tigers * "Marie" (Cat Mother and the All Night Newsboys song), 1969 * "Marie" (Johnny Hallyday song), 2002 * "Marie" (Sleepy Hallow song), 2022 * "Marie" ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Commission
The European Commission (EC) is the primary Executive (government), executive arm of the European Union (EU). It operates as a cabinet government, with a number of European Commissioner, members of the Commission (directorial system, informally known as "commissioners") corresponding to two thirds of the number of Member state of the European Union, member states, unless the European Council, acting unanimously, decides to alter this number. The current number of commissioners is 27, including the president. It includes an administrative body of about 32,000 European civil servants. The commission is divided into departments known as Directorate-General, Directorates-General (DGs) that can be likened to departments or Ministry (government department), ministries each headed by a director-general who is responsible to a commissioner. Currently, there is one member per European Union member state, member state, but members are bound by their oath of office to represent the genera ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PeptideAtlas
PeptideAtlas is a proteomics data resource that gathers tandem mass spectrometry datasets from around the world, reprocesses them with the Trans-Proteomic Pipeline, and makes the combined result freely available to the community. Peptide Atlas is one of the founding members of the ProteomeXchange Consortium. History The earliest conception of PeptideAtlas began at the Institute for Systems Biology in the research lab of Ruedi Aebersold by Eric Deutsch and Sharon Chen at the Annotated Peptide Database (APD). The concept was further expanded with additional efforts from Parag Mallick and Frank Desiere. The first instance for an ensemble of human experiments was published in 2004 as the Human PeptideAtlas. The concept was further expanded to many other species over the years with major effort by Nichole King, Zhi Sun, Terry Farrah, and Dave Campbell. Current status PeptideAtlas is still maintained and developed at the Institute for Systems Biology in the research lab of Robert ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Human Proteinpedia
Human Proteinpedia, which is closely associated with Institute of Bioinformatics (IOB), Bangalore and Johns Hopkins University, is a portal for sharing and integration of human proteomic data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information at the context of an individual protein. In essence, researchers can add new data to HPRD by registering to Human Proteinpedia. The data deposited in Human Proteinpedia is freely available for download. Emphasizing the importance of proteomics data disposition to public repositories, ''Nature Methods'' recommends Human Proteinpedia in their editorial.Editorial. Thou shalt share your data. Nat Methods. 2008 Mar;5:209 More than 70 labs participate in this effort. Data types Data pertaining to post-translational modifications, protein–protein interactions, tissue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Drosophila Melanogaster
''Drosophila melanogaster'' is a species of fly (an insect of the Order (biology), order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly", "pomace fly", or "banana fly". In the wild, ''D. melanogaster'' are attracted to rotting fruit and fermenting beverages, and are often found in orchards, kitchens and pubs. Starting with Charles W. Woodworth's 1901 proposal of the use of this species as a model organism, ''D. melanogaster'' continues to be widely used for biological research in genetics, physiology, microbial pathogenesis, and Life history theory, life history evolution. ''D. melanogaster'' was the first animal to be Fruit flies in space, launched into space in 1947. As of 2017, six Nobel Prizes have been awarded to drosophilists for their work using the insect. ''Drosophila melanogaster'' is typically used in research owing to its rapid life cycle, relatively simple genetics with on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics Standards Initiative
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification. The Proteomics Standards Initiative focuses on the following subjects: minimum information about a proteomics experiment defines the metadata that should be provided along with a proteomics experiment. a data markup language for encoding the data, and metadata ontologies for consistent annotation and representation. Minimum information about a proteomics experiment Minimum information about a proteomics experiment (MIAPE) is a minimum information standard, created by the Proteomics Standards Initiative of the Human Proteome Organization, for reporting proteomics experiments. You can't just introduce the results of an analysis, it is intended to specify all the information necessary to interpret the experiment results unambiguously and to potentially reproduce the experiment. Wh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MzML
Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins (proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here. O ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Programming Language
Java is a high-level, general-purpose, memory-safe, object-oriented programming language. It is intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. Java gained popularity shortly after its release, and has been a popular programming language since then. Java was the third most popular programming language in according to GitHub. Although still widely popular, there has been a gradual decline in use of Java in recent years with other ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache License
The Apache License is a permissive free software license written by the Apache Software Foundation (ASF). It allows users to use the software for any purpose, to distribute it, to modify it, and to distribute modified versions of the software under the terms of the license, without concern for royalties. The ASF and its projects release their software products under the Apache License. The license is also used by many non-ASF projects. History Beginning in 1995, the Apache Group (later the Apache Software Foundation) released successive versions of the Apache HTTP Server. Its initial license was essentially the same as the original 4-clause BSD license, with only the names of the organizations changed, and with an additional clause forbidding derivative works from bearing the Apache name. In July 1999, the Berkeley Software Distribution accepted the argument put to it by the Free Software Foundation and retired their ''advertising clause'' (clause 3) to form the new 3-clau ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
