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ProteoWizard
ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses. It provides a framework for unified mass spectrometry data file access and performs standard chemistry and LCMS dataset computations. Specifically, it is able to read many of the vendor-specific, proprietary formats and converting the data into an open data format. On the application level, the software provides executables for data conversion (msConvert, msConvertGUI and idConvert), data visualization (msPicture and seeMS), data access (msAccess, msCat, idCat and msPicture), data analysis (peekaboo and msPrefix14) and basic proteomics utilities (chainsaw). In addition, the project also hosts the Skyline software which helps to create, acquire and analyze targeted proteomics experiments such as SRM experiments. The main contributors to the project are the Tabb, MacCoss and Mallick research labs as well as Insilicos. See also * OpenMS * Trans-Proteomic Pipeline The Trans-Pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenMS
OpenMS is an open-source project for data analysis and processing in mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, MacOS and Linux. OpenMS has tools for analysis of proteomics data, providing algorithms for signal processing, feature finding (including de-isotoping), visualization in 1D (spectra or chromatogram level), 2D and 3D, map mapping and peptide identification. It supports label-free and isotopic-label based quantification (such as iTRAQ and TMT and SILAC). OpenMS also supports metabolomics workflows and targeted analysis of DIA/SWATH data. Furthermore, OpenMS provides tools for the analysis of cross linking data, including protein-protein, protein-RNA and protein-DNA cross linking. Lastly, OpenMS provides tools for analysis of RNA mass spectrometry data. History OpenMS was originally released in 2007 in version 1.0 and was described in two articles published in Bioinformati ... [...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] |
Trans-Proteomic Pipeline
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra. Software Components Probability Assignment and Validation PeptideProphet performs statistical validation of peptide-spectra-matches (PSM) using the results of search engines by estimating a false discovery rate (FDR) on PSM level. The initial PeptideProphet used a fit of a Gaussian distribution for the correct identifications and a fit of a gamma distribution In probability theory and statistics, the gamma distribution is a two-parameter family of continuous probability distributions. The exponential distribution, Erlang distribution, and chi-square distribution are special cases of the gamma distri ... for the incorrect identification. A later modification of the program allowed the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C Sharp (programming Language)
C# (pronounced ) is a general-purpose, high-level multi-paradigm programming language. C# encompasses static typing, strong typing, lexically scoped, imperative, declarative, functional, generic, object-oriented ( class-based), and component-oriented programming disciplines. The C# programming language was designed by Anders Hejlsberg from Microsoft in 2000 and was later approved as an international standard by Ecma (ECMA-334) in 2002 and ISO/ IEC (ISO/IEC 23270) in 2003. Microsoft introduced C# along with .NET Framework and Visual Studio, both of which were closed-source. At the time, Microsoft had no open-source products. Four years later, in 2004, a free and open-source project called Mono began, providing a cross-platform compiler and runtime environment for the C# programming language. A decade later, Microsoft released Visual Studio Code (code editor), Roslyn (compiler), and the unified .NET platform (software framework), all of which support C# and are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Windows
Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for servers, and Windows IoT for embedded systems. Defunct Windows families include Windows 9x, Windows Mobile, and Windows Phone. The first version of Windows was released on November 20, 1985, as a graphical operating system shell for MS-DOS in response to the growing interest in graphical user interfaces (GUIs). Windows is the most popular desktop operating system in the world, with 75% market share , according to StatCounter. However, Windows is not the most used operating system when including both mobile and desktop OSes, due to Android's massive growth. , the most recent version of Windows is Windows 11 for consumer PCs and tablets, Windows 11 Enterprise for corporations, and Windows Server 2022 for servers. Genealogy By ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OS X
macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and laptop computers it is the second most widely used desktop OS, after Microsoft Windows and ahead of ChromeOS. macOS succeeded the classic Mac OS, a Mac operating system with nine releases from 1984 to 1999. During this time, Apple cofounder Steve Jobs had left Apple and started another company, NeXT, developing the NeXTSTEP platform that would later be acquired by Apple to form the basis of macOS. The first desktop version, Mac OS X 10.0, was released in March 2001, with its first update, 10.1, arriving later that year. All releases from Mac OS X 10.5 Leopard and after are UNIX 03 certified, with an exception for OS X 10.7 Lion. Apple's other operating systems ( iOS, iPadOS, watchOS, tvOS, audioOS) are derivatives of macOS. A p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ... [...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 propertie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Selected 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+. Th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Science Software
Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procure political rights, as for a disenfranchised group * Free will, control exercised by rational agents over their actions and decisions * Free of charge, also known as gratis. See Gratis vs libre. Computing * Free (programming), a function that releases dynamically allocated memory for reuse * Free format, a file format which can be used without restrictions * Free software, software usable and distributable with few restrictions and no payment * Freeware, a broader class of software available at no cost Mathematics * Free object ** Free abelian group ** Free algebra ** Free group ** Free module ** Free semigroup * Free variable People * Free (surname) * Free (rapper) (born 1968), or Free Marie, American rapper and media perso ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
The list of bioinformatics software tools can be split up according to the license used: * List of proprietary bioinformatics software *List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software **List of sequence alignment software **List of alignment visualization software **Alignment-free sequence analysis **De novo sequence assemblers **List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools ** List of phylogenetics software ** List of phylogenetic tree visualization software ** :Metagenomics_software *Structural biology software **List of molecular graphics systems **List of protein-ligand docking software ** List of RNA structure prediction software ** List of software for protein model error verification **List of protein secondary structure prediction programs **List of protein st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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