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XCMS Online
XCMS Online is a cloud version of the original XCMS technology (a bioinformatics software designed for statistical analysis of mass spectrometry data), created by the Siuzdak Lab at Scripps Research. XCMS introduced the concept of nonlinear retention time alignment that allowed for the statistical assessment of the detected peaks across LCMS and GCMS datasets. XCMS Online was designed to facilitate XCMS analyses through a cloud portal and as a more straightforward (non command driven) way to analyze, visualize and share untargeted metabolomic data. Further to this, the combination of XCMS and METLIN allows for the identification of known molecules using METLIN's tandem mass spectrometry data, and enables the identification of unknown (uncharacterized molecules) via similarity searching of tandem mass spectrometry data. XCMS Online has also become a systems biology tool for integrating different omic data sets. As of January 2021, thXCMSOnline/METLIN platform has over 44,000 regis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
XCMS Alignment
The X Window System core protocolRobert W. Scheifler and James Gettys: ''X Window System: Core and extension protocols, X version 11, releases 6 and 6.1'', Digital Press 1996, RFC 1013Grant EdwardsAn Introduction to X11 User Interfaces/ref> is the base protocol of the X Window System, which is a Computer network, networked windowing system for bitmap displays used to build graphical user interfaces on Unix, Unix-like, and other operating systems. The X Window System is based on a client–server model: a single Server (computing), server controls the input/output hardware, such as the Computer screen, screen, the Computer keyboard, keyboard, and the Computer mouse, mouse; all application Computer program, programs act as client (computing), clients, interacting with the user (computing), user and with the other clients via the server. This interaction is regulated by the X Window System core protocol. Other protocol (computing), protocols related to the X Window System exist, both bu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Web Platform
The Web platform is a collection of technologies developed as open standards by the World Wide Web Consortium and other standardization bodies such as the Web Hypertext Application Technology Working Group, the Unicode Consortium, the Internet Engineering Task Force, and Ecma International. It is the umbrella term introduced by the World Wide Web Consortium, and in 2011 it was defined as "a platform for innovation, consolidation and cost efficiencies" by W3C CEO Jeff Jaffe. Being built oThe evergreen Web(where rapid, automatic software updates, vendor co-operation, standardization, and competition take place) has allowed for the addition of new capabilities while addressing security and privacy risks. Additionally, developers are enabled to build interoperable content on a cohesive platform. The Web platform includes technologies—computer languages and APIs—that were originally created in relation to the publication of Web pages. This includes HTML, CSS, SVG, MathML, WAI-ARIA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry Software
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. Proteomics software In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and ''de novo'' search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data. Database search algorithms De novo sequencing algorithms De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels ''et al.'' (1990). Homology searching algorithms MS/MS peptide quantification Other software See also * Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters. * List of protein ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Freemium
Freemium, a portmanteau of the words "free" and "premium," is a pricing strategy by which a basic product or service is provided free of charge, but money (a premium) is charged for additional features, services, or virtual (online) or physical (offline) goods that expand the functionality of the free version of the software. This business model has been used in the software industry since the 1980s. A subset of this model used by the video game industry is called free-to-play. Origin The business model has been in use for software since the 1980s. The term ''freemium'' to describe this model appears to have been created only much later, in response to a 2006 blog post by venture capitalist Fred Wilson summarizing the model:Give your service away for free, possibly ad supported but maybe not, acquire a lot of customers very efficiently through word of mouth, referral networks, organic search marketing, etc., then offer premium-priced value-added services or an enhanced version o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Commercial Software
Commercial software, or seldom payware, is a computer software that is produced for sale or that serves commercial purposes. Commercial software can be proprietary software or free and open-source software. Background and challenge While software creation by programming is a time and labor-intensive process, comparable to the creation of physical goods, the reproduction, duplication and sharing of software as digital goods is in comparison disproportionately easy. No special machines or expensive additional resources are required, unlike almost all physical goods and products. Once a software is created it can be copied in infinite numbers, for almost zero cost, by anyone. This made commercialization of software for the mass market in the beginning of the computing era impossible. Unlike hardware, it was not seen as trade-able and commercialize-able good. Software was plainly shared for free (hacker culture) or distributed bundled with sold hardware, as part of the service t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scripps Research
Scripps Research, previously known as The Scripps Research Institute (TSRI), is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institute has over 170 laboratories employing 2,100 scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. The institute holds over 1,100 patents, has produced 11 FDA-approved therapeutics, and has generated over 50 spin-off companies. According to the 2017 Nature Innovation Index, Scripps Research is the #1 most influential research institution in the world. The Scripps Research graduate program is ranked 9th nationally in the biological sciences, 6th for organic chemistry, and 6th for biochemistry. In 2022, their Jupiter, FL campus became a part of the University of Florida. Jupiter-based ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
METLIN
The METLIN Metabolite and Chemical Entity Database is the largest repository of experimental tandem mass spectrometry and neutral loss data acquired from standards. The tandem mass spectrometry data on over 870,000 molecular standards (as of August 16, 2022) is provided to facilitate the identification of chemical entities from tandem mass spectrometry experiments. In addition to the identification of known molecules it is also useful for identifying unknowns using its similarity searching technology. All tandem mass spectrometry data comes from the experimental analysis of standards at multiple collision energies and in both positive and negative ionization modes. METLIN serves as a data management system to assist in metabolite and chemical entity identification by providing public access to its repository of comprehensive MS/MS and neutral loss data. METLIN's annotated list of molecular standards include metabolites and other chemical entities, searching METLIN can be done base ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Danaher Corporation
Danaher Corporation is an American globally diversified conglomerate with its headquarters in Washington, D.C. The company designs, manufactures, and markets professional, medical, industrial, and commercial products and services. The company's 3 platforms are " Life Sciences", "Diagnostics", and "Environmental & Applied Solutions". Danaher is ranked 130th on the Fortune 500 2021. The company is named after Danaher Creek in Western Montana. Founders Steven M. Rales and Mitchell Rales first conceptualized the company while fishing there. Danaher was one of the first companies in North America to adopt " Kaizen" principles to manufacturing, which is a lean manufacturing Japanese philosophy of continuous improvement, and elimination of waste. History The company was organized in 1969 as a Massachusetts real estate investment trust under its former name DMG, Inc. In 1978, DMG, Inc. was reorganized as a Florida corporation and changed its name to Diversified Mortgage Investors, ... [...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. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent property, emergent properties, properties of cell (biology), cells, tissue (biology), tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Reaction Monitoring
Selected reaction monitoring (SRM), also called Multiple reaction monitoring, (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product of a fragmentation reaction of the precursor ions is selected in the second mass spectrometer stage for detection. Variants A general case of SRM can be represented by :ABCD^+ \to AB + CD^+ where the precursor ion ABCD+ is selected by the first stage of mass spectrometry (MS1), dissociates into molecule AB and product ion CD+, and the latter is selected by the second stage of mass spectrometry (MS2) and detected. The precursor and product ion pair is called a SRM "transition." Consecutive reaction monitoring (CRM) is the serial application of three or more stages of mass spectrometry to SRM, represented in a simple case by :ABCD^+ \to AB + CD^+ \to C + D^+ where ABCD+ is selected by MS1, dissociates into molecule AB and ion CD+. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
