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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] |
Institute For Systems Biology
Institute for Systems Biology (ISB) is a non-profit research institution located in Seattle, Washington, United States. ISB concentrates on systems biology, the study of relationships and interactions between various parts of biological systems, and advocates an interdisciplinary approach to biological research. Goals Systems biology is the study of biological systems in a holistic manner by integrating data at all levels of the biological information hierarchy, from global down to the individual organism, and below down to the molecular level. The vision of ISB is to integrate these concepts using a cross-disciplinary approach combining the efforts of biologists, chemists, computer scientists, engineers, mathematicians, physicists, and physicians. On its website, ISB has defined four areas of focus: * P4 Medicine - This acronym refers to predictive, preventive, personalized and participatory medicine, which focuses on wellness rather than mere treatment of disease. * Global He ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of 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 functional genomi ... [...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] |
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] |
False Discovery Rate
In statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the expected proportion of "discoveries" (rejected null hypotheses) that are false (incorrect rejections of the null). Equivalently, the FDR is the expected ratio of the number of false positive classifications (false discoveries) to the total number of positive classifications (rejections of the null). The total number of rejections of the null include both the number of false positives (FP) and true positives (TP). Simply put, FDR = FP / (FP + TP). FDR-controlling procedures provide less stringent control of Type I errors compared to family-wise error rate (FWER) controlling procedures (such as the Bonferroni correction), which control the probability of ''at least one'' Type I error. Thus, FDR-controlling procedures have greater power, at th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 distribution. There are two equivalent parameterizations in common use: #With a shape parameter k and a scale parameter \theta. #With a shape parameter \alpha = k and an inverse scale parameter \beta = 1/ \theta , called a rate parameter. In each of these forms, both parameters are positive real numbers. The gamma distribution is the maximum entropy probability distribution (both with respect to a uniform base measure and a 1/x base measure) for a random variable X for which E 'X''= ''kθ'' = ''α''/''β'' is fixed and greater than zero, and E n(''X'')= ''ψ''(''k'') + ln(''θ'') = ''ψ''(''α'') − ln(''β'') is fixed (''ψ'' is the digamma function). Definitions The parameterization with ''k'' and ''θ'' appears to be more common ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Normal Distribution
In statistics, a normal distribution or Gaussian distribution is a type of continuous probability distribution for a real-valued random variable. The general form of its probability density function is : f(x) = \frac e^ The parameter \mu is the mean or expectation of the distribution (and also its median and mode), while the parameter \sigma is its standard deviation. The variance of the distribution is \sigma^2. A random variable with a Gaussian distribution is said to be normally distributed, and is called a normal deviate. Normal distributions are important in statistics and are often used in the natural and social sciences to represent real-valued random variables whose distributions are not known. Their importance is partly due to the central limit theorem. It states that, under some conditions, the average of many samples (observations) of a random variable with finite mean and variance is itself a random variable—whose distribution converges to a normal dist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
False Discovery Rate
In statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the expected proportion of "discoveries" (rejected null hypotheses) that are false (incorrect rejections of the null). Equivalently, the FDR is the expected ratio of the number of false positive classifications (false discoveries) to the total number of positive classifications (rejections of the null). The total number of rejections of the null include both the number of false positives (FP) and true positives (TP). Simply put, FDR = FP / (FP + TP). FDR-controlling procedures provide less stringent control of Type I errors compared to family-wise error rate (FWER) controlling procedures (such as the Bonferroni correction), which control the probability of ''at least one'' Type I error. Thus, FDR-controlling procedures have greater power, at th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ruedi Aebersold
Rudolf Aebersold (better known as Ruedi Aebersold born September 12, 1954 ) is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. He was one of the founders of the Institute for Systems Biology in Seattle, Washington, where he previously had a research group. Ruedi Aebersold is known for the development and application of targeted proteomics techniques in the field of biomedical research, in order to understand the function, interaction and localization of each protein in the cell and its changes in disease states. To this end, Ruedi Abersold has made significant contributions in the development and application of targeted proteomics methods, including selected reaction monitoring and data-independent acquisi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Perl
Perl is a family of two High-level programming language, high-level, General-purpose programming language, general-purpose, Interpreter (computing), interpreted, dynamic programming languages. "Perl" refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned "sister language", Perl 6, before the latter's name was officially changed to Raku (programming language), Raku in October 2019. Though Perl is not officially an acronym, there are various backronyms in use, including "Practical Data extraction, Extraction and Reporting Language". Perl was developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions. Raku, which began as a redesign of Perl 5 in 2000, eventually evolved into a separate language. Both languages continue to be developed independently by different development teams and liberally borrow ideas from each other. The Perl languages borrow featur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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