In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long protein coding genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the Center for Computational Biology at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White. == Versions == === GLIMMER 1.0 === First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper Microbial gene identification using interpolated Markov model. Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the local composition sequence dependencies which makes GLIMMER more flexible and more powerful when compared to fixed-order Markov model. There was a comparison made between interpolated Markov model used by GLIMMER and fifth order Markov model in the paper Microbial gene identification using interpolated Markov models. "GLIMMER algorithm found 1680 genes out of 1717 annotated genes in Haemophilus influenzae where fifth order Markov model found 1574 genes. GLIMMER found 209 additional genes which were not included in 1717 annotated genes where fifth order Markov model found 104 genes."' === GLIMMER 2.0 === Second Version of GLIMMER i.e., GLIMMER 2.0 was released in 1999 and it was published in the paper Improved microbial identification with GLIMMER. This paper provides significant technical improvements such as using interpolated context model instead of interpolated Markov model and resolving overlapping genes which improves the accuracy of GLIMMER. Interpolated context models are used instead of interpolated Markov model which gives the flexibility to select any base. In interpolated Markov model probability distribution of a base is determined from the immediate preceding bases. If the immediate preceding base is irrelevant amino acid translation, interpolated Markov model still considers the preceding base to determine the probability of given base where as interpolated context model which was used in GLIMMER 2.0 can ignore irrelevant bases. False positive predictions were increased in GLIMMER 2.0 to reduce the number of false negative predictions. Overlapped genes are also resolved in GLIMMER 2.0. Various comparisons between GLIMMER 1.0 and GLIMMER 2.0 were made in the paper Improved microbial identification with GLIMMER which shows improvement in the later version. "Sensitivity of GLIMMER 1.0 ranges from 98.4 to 99.7% with an average of 99.1% where as GLIMMER 2.0 has a sensitivity range from 98.6 to 99.8% with an average of 99.3%. GLIMMER 2.0 is very effective in finding genes of high density. The parasite Trypanosoma brucei, responsible for causing African sleeping sickness is being identified by GLIMMER 2.0" === GLIMMER 3.0 === Third version of GLIMMER, "GLIMMER 3.0" was released in 2007 and it was published in the paper Identifying bacterial genes and endosymbiont DNA with Glimmer. This paper describes several major changes made to the GLIMMER system including improved methods to identify coding regions and start codon. Scoring of ORF in GLIMMER 3.0 is done in reverse order i.e., starting from stop codon and moves back towards the start codon. Reverse scanning helps in identifying the coding portion of the gene more accurately which is contained in the context window of IMM. GLIMMER 3.0 also improves the generated training set data by comparing the long-ORF with universal amino acid distribution of widely disparate bacterial genomes."GLIMMER 3.0 has an average long-ORF output of 57% for various organisms where as GLIMMER 2.0 has an average long-ORF output of 39%." GLIMMER 3.0 reduces the rate of false positive predictions which were increased in GLIMMER 2.0 to reduce the number of false negative predictions. "GLIMMER 3.0 has a start-site prediction accuracy of 99.5% for 3'5' matches where as GLIMMER 2.0 has 99.1% for 3'5' matches. GLIMMER 3.0 uses a new algorithm for scanning coding regions, a new start site detection module, and architecture which integrates all gene predictions across an entire genome." Minimum description length === Theoretical and Biological Foundation === The GLIMMER project helped introduce and popularize the use of variable length models in Computational Biology and Bioinformatics that subsequently have been applied to numerous problems such as protein classification and others. Variable length modeling was originally pioneered by information theorists and subsequently ingeniously applied and popularized in data compression (e.g. Ziv-Lempel compression). Prediction and compression are intimately linked using Minimum Description Length Principles. The basic idea is to create a dictionary of frequent words (motifs in biological sequences). The intuition is that the frequently occurring motifs are likely to be most predictive and informative. In GLIMMER the interpolated model is a mixture model of the probabilities of these relatively common motifs. Similarly to the development of HMMs in Computational Biology, the authors of GLIMMER were conceptually influenced by the previous application of another variant of interpolated Markov models to speech recognition by researchers such as Fred Jelinek (IBM) and Eric Ristad (Princeton). The learning algorithm in GLIMMER is different from these earlier approaches. == Access == GLIMMER can be downloaded from The Glimmer home page (requires a C++ compiler). Alternatively, an online version is hosted by NCBI [1]. == How it works == GLIMMER primarily searches for long-ORFS. An open reading frame might overlap with any other open reading frame which will be resolved using the technique described in the sub section. Using these long-ORFS and following certain amino acid distribution GLIMMER generates training set data. Using these training data, GLIMMER trains all the six Markov models of coding DNA from zero to eight order and also train the model for noncoding DNA GLIMMER tries to calculate the probabilities from the data. Based on the number of observations, GLIMMER determines whether to use fixed order Markov model or interpolated Markov model. If the number of observations are greater than 400, GLIMMER uses fixed order Markov model to obtain there probabilities. If the number of observations are less than 400, GLIMMER uses interpolated Markov model which is briefly explained in the next sub section. GLIMMER obtains score for every long-ORF generated using all the six coding DNA models and also using non-coding DNA model. If the score obtained in the previous step is greater than a certain threshold then GLIMMER predicts it to be a gene. The steps explained above describes the basic functionality of GLIMMER. There are various improvements made to GLIMMER and some of them are described in the following sub-sections. === The GLIMMER system === GLIMMER system consists of two programs. First program called build-imm, which takes an input set of sequences and outputs the interpolated Markov model as follows. The probability for each base i.e., A,C,G,T for all k-mers for 0 ≤ k ≤ 8 is computed. Then, for each k-mer, GLIMMER computes weight. New sequence probability is computed as follows. where n is the length of the sequence S x {\displaystyle S_{x}} is the oligomer at position x. I M M 8 ( S x ) {\displaystyle IMM_{8}(S_{x})} , the 8 t h {\displaystyle 8^{th}} -order interpolated Markov model score is computed as "where Y k ( S x − 1 ) {\displaystyle Y_{k}(S_{x-1})} is the weight of the k-mer at position x-1 in the sequence S and P k ( S x ) {\displaystyle P_{k}(S_{x})} is the estimate obtained from the training data of the probability of the base located at position x in the k t h {\displaystyle k^{th}} -order model." The probability of base S x {\displaystyle S_{x}} given the i previous bases is computed as follows. "The value of Y i ( S x ) {\displaystyle Y_{i}(S_{x})} associated with P i ( S x ) {\displaystyle P_{i}(S_{x})} can be regarded as a measure of confidence in the accuracy of this value as an estimate of the true probability. GLIMMER uses two criteria to determine Y i ( S x ) {\displaystyle Y_{i}(S_{x})} . The first of these is simple frequency occurrence in which the number of occurrences of context string S x , i {\displaystyle S_{x,i}} in the training data exceeds a specific threshold value, then Y i ( S x ) {\displaystyle Y_{i}(S_{x})} is set to 1.0. The current default value for threshold is 400, which gives 95% confidence. When there are insufficient sample occurrences of a context string, build-imm employ additional criteria to determine Y {\displaystyle Y} value. For a
Latent semantic mapping
Latent semantic mapping (LSM) is a data-driven framework to model globally meaningful relationships implicit in large volumes of (often textual) data. It is a generalization of latent semantic analysis. In information retrieval, LSA enables retrieval on the basis of conceptual content, instead of merely matching words between queries and documents. LSM was derived from earlier work on latent semantic analysis. There are 3 main characteristics of latent semantic analysis: Discrete entities, usually in the form of words and documents, are mapped onto continuous vectors, the mapping involves a form of global correlation pattern, and dimensionality reduction is an important aspect of the analysis process. These constitute generic properties, and have been identified as potentially useful in a variety of different contexts. This usefulness has encouraged great interest in LSM. The intended product of latent semantic mapping, is a data-driven framework for modeling relationships in large volumes of data. Mac OS X v10.5 and later includes a framework implementing latent semantic mapping.
Microsoft Office PerformancePoint Server
Microsoft Office PerformancePoint Server is a business intelligence software product released in 2007 by Microsoft. The product was generally an integration of the acquisitions from ProClarity - the Planning Server and Monitoring Server - into Microsoft's SharePoint server product line. Although discontinued in 2009, the dashboard, scorecard, and analytics capabilities of PerformancePoint Server were incorporated into SharePoint 2010 and later versions. PerformancePoint Server also provided a planning and budgeting component directly integrated with Excel. == History == Microsoft offered preview releases of PerformancePoint Server starting in mid-2006. Previews of the product were formed from Business Scorecard Manager 2005 and the Planning Server component. Acquisitions ProClarity and Great Plains brought additional analytics and planning/reporting capabilities, as well as companion products ProClarity 6.3 and FRx. PerformancePoint Server was officially released in November 2007. Microsoft discontinued PerformancePoint Server as an independent product in 2009 and folded its dashboard, scorecard and analytics capabilities into PerformancePoint Services in SharePoint Server 2010. == Monitoring Server Component == Business monitoring capabilities, including dashboards, scorecards & key performance indicators, navigable reports for deeper analysis, strategy maps, and linked filtering, are provided by PerformancePoint's Monitoring Server component. A Dashboard Designer application that is distributed from Monitoring Server enables business analysts or IT Administrators to: create & test data source connections create views that use those data connections assemble the views into a dashboard deploy the dashboard as a SharePoint page Dashboard Designer saved content and security information back to the Monitoring Server. Data source connections, such as OLAP cubes or relational tables, were also made through Monitoring Server. After a dashboard has been published to the Monitoring Server database, it would be deployed as a SharePoint page and shared with other users as such. When the pages were opened in a web browser, Monitoring Server updated the data in the views by connecting back to the original data sources. == Planning Server Component == PerformancePoint's Planning Server component supported maintenance of logical business models, budget & approval workflows, enterprise data sources, and it followed Generally Accepted Accounting Principles. Planning Server made use of Excel for input and line-of-business reporting, as well as SQL Server for storing and processing business models. == Management Reporter Component == The Management Reporter component was designed to perform financial reporting and can read PerformancePoint Planning models directly. A development kit was also available to allow this component to read other models.
Novell File Reporter
Novell File Reporter (NFR) is software that allows network administrators to identify files stored on the network and generates reports regarding the size of individual files, file type, when files were last accessed, and where duplicates exist. Additionally, the File Reporter tracks storage volume capacity and usage. It is a component of the Novell File Management Suite. == How it works == Novell File Reporter examines and reports on terabytes of data via a central reporting engine (NFR Engine) and distributed agents (NFR Agents). The NFR Engine schedules the scans of file instances conducted by NFR Agents, processes and compiles the scans for reporting purposes, and provides report information to the user interface. In addition to the standard reports it can generate, the NFR Engine can also produce "trigger reports" in response to specific events (a server volume crossing a capacity threshold, for example). Accordingly, the NFR Engine monitors the data gathered by the NFR Agents in order to identify these "triggers." The NFR Engine when working in either eDirectory or Active Directory connects to the directory via a Directory Services Interface (DSI) and thus can monitor and check file permissions.
Informedia Digital Library
The Informedia Digital Library is an ongoing research program at Carnegie Mellon University to build search engines and information visualization technology for many types of media. The program has carried out research on spoken document retrieval, video information retrieval, video segmentation, face recognition, and cross-language information retrieval. The Lycos search engine was an early product of the Informedia Digital Library Project. The project is led by Howard Wactlar. Researchers on the project have included: Michael Mauldin, Alex Hauptmann, Michael Christel, Michael Witbrock, Raj Reddy, Takeo Kanade and Scott Stevens.
Reference Software International
Reference Software International, Inc. (RSI), was an American software developer active from 1985 to 1993 and based in Albuquerque, New Mexico, and San Francisco, California. The company released several productivity and reference software packages, including the Grammatik grammar checker, for MS-DOS. The company was acquired by WordPerfect Corporation in 1993. == History == === Background (1980–1985) === Reference Software International, Inc., was founded by Donald "Don" Emery and Bruce Wampler in 1985 in San Francisco, California. Both Wampler and Emery were college professors when they founded RSI: Wampler at the University of New Mexico as a professor of computer science and Emery a professor of marketing at San Francisco State University. After graduating from the University of Utah in around 1978, Wampler founded his first software company, Aspen Software, in Tijeras, New Mexico, in 1979. Wampler founded Aspen to develop an early spell checker software package, called Proofreader, for the TRS-80, licensing Random House's Webster's Unabridged Dictionary for the package's lexicon. In 1980, he began development on a grammar checker inspired by Writer's Workbench, a pioneering grammar checker for Unix systems. Wampler used Writer's Workbench heavily during the writer of his doctoral dissertation but disliked having to jump between the Apple II on which he composed the dissertation and the mainframe on which Writer's Workbench ran, and so wanted to develop a version of the latter for microcomputers. Wampler's work came to fruition as Grammatik in 1981, eventually ported to several other microcomputer platforms in the early 1980s. In 1983, by which point the company had 12 employees and sold a combined 80,000 units of Grammatik and Proofreader, Wampler sold Aspen to Dictronics, a software company best known for developing the Electronic Thesaurus, an early thesaurus program for microcomputers. Dictronics was in turn purchased by Wang Laboratories; according to Wampler, "Wang bought [Aspen] and sat on it. They did nothing with it". Wampler moved on to teach for the University of New Mexico, but, frustrated by Wang's inaction, got the urge to resurrect his work. In 1985, he was able to license back Grammatik and Proofreader from a small California-based software firm that had grandfathered rights to a forked version of both. In the same year, he met Emery, who, impressed by Wampler's, founded Reference Software International to market his software. RSI's research and development headquarters were based in Albuquerque, while the company's sales and marketing department was based in Walnut Creek, California. === Success (1985–1992) === In August 1985, RSI released their first product: the Random House Reference Set, a new version of Proofreader for the IBM Personal Computer and compatibles, revised to be a terminate-and-stay-resident program that ran atop other word processors such as WordStar or WordPerfect. At the time, Reference Set was the only such program on the market that functioned like this. RSI netted $114,000 from sales of Reference Set by the end of 1985. In June 1986, they released version 2.0 of Grammatik as Grammatik II for the PC. The latter was a breakout hit for RSI, receiving praise in the press (including technology journals such as PC Magazine) and RSI selling 1,000 units a month. In spring 1987, they released Reference Set II, which allowed users to import their own words into the built-in dictionary and added a thesaurus of 300,000 words. In November 1987, they released version 3.0 of Reference Set, which comprised two new field-specific dictionaries for the medical and legal professions. As well as the general Random House dictionary and thesaurus, it included Stedman's Medical Dictionary and Black's Law Dictionary. Emery consulted Paul Brest and Bob Jackson—professors of law at Stanford Law School and San Francisco State respectively—for the curation of the law dictionary; and Burton Grebin—at the time the executive director of Mount Saint Mary's Hospital—for the curation of the medical dictionary. In fall 1988, the company released Grammatik III, a total rewrite that made use of artificial intelligence to more accurately judge the grammar of sentences by breaking them down into a syntactic hierarchy. Grammatik III received universal acclaim, with Gloria Morris of InfoWorld calling it the apparent leader in the grammar checking field and Sandra Anderson of Mac Home Journal calling it "hands down ... the best of the industry" six years after its release. By 1989, the product had competitors in Correct Grammar by Lifetree Software and RightWriter by Rightsoft, Inc. By 1990, RSI achieved annual sales of $9.7 million. In the same year they released Grammatik IV, which was the first to offer direct integration with WordPerfect on both MS-DOS and Windows. In March 1992—by which point RSI had sold 1.5 million copies of Grammatik across all versions—the company released version 5 of the program, another rewrite that updated the lexicon further and added new functions such as word redundancy detection. Around the same time, the company introduced Easy Proof, a pared-down version of Grammatik intended for novice writers, students, and family computers. In 1991, the company was engaged in a trademark dispute with Systems Compatibility Corporation (SCC) of Chicago, Illinois, over the rights to the Software Toolkit title. Both companies had published software bundles bearing the name in the turn of the 1990s; SCC had published theirs first in 1988 and registered the trademark with the USPTO. SCC was granted a restraining order against RSI in January 1991. The following month, RSI agreed to rename their product, preventing a protracted legal battle. === Decline and acquisition (1992–1993) === By early 1992, RSI achieved annual sales of more than $13 million, employed 120 people, and had opened international offices in London, Belgium, and Antwerp to sell foreign versions of Reference Set and Grammatik. The company reached peak employment in the middle of 1992, with 140 employees. However, RSI's launch of six disparate titles in the year proved problematic for the company when they failed to sell as well as they had projected, and the company laid off employees by the dozens. By December 1992, only 71 employees were left, 32 from their San Francisco office. On the last day of 1992, RSI received an acquisition offer from WordPerfect Corporation, makers of the namesake word processor based in Orem, Utah. The deal was inked in January 1993, RSI's stakeholders receiving $19 million. The company's remaining employees were absorbed into WordPerfect in Orem. WordPerfect continued selling Grammatik as a standalone product for several years.
Manhattan address algorithm
The Manhattan address algorithm is a series of formulas used to estimate the closest east–west cross street for building numbers on north–south avenues in the New York City borough of Manhattan. == Algorithm == To find the approximate number of the closest cross street, divide the building number by a divisor (generally 20) and add (or subtract) the "tricky number" from the table below: For the north–south avenues, there are typically 20 address numbers between consecutive east–west streets (10 on either side of the avenue). A standard land lot on each avenue was originally 20 feet (6.1 m) wide, and there is about 200 feet (61 m) between each pair of east–west streets, for ten land lots between each pair of streets. The exceptions are Riverside Drive, as well as Fifth Avenue and Central Park West between 59th and 110th streets, which use a divisor of 10. These avenues all have buildings only on one side of the street, with a park on the other side. The "tricky number" often corresponds to a street near the southern end of the avenue. There are some notable exceptions: York Avenue address numbers are continuations of Avenue A address numbers, since the avenue was originally called Avenue A. East End Avenue address numbers are continuations of Avenue B address numbers, since the avenue was originally called Avenue B. Sixth Avenue and Broadway start south of Houston Street, the southern boundary of the Manhattan street numbering system. Although Park Avenue's southern terminus is at 32nd Street, a homeowner at 34th Street wanted the address "1 Park Avenue" (this was later changed). === Examples === For example, if you are at 62 Avenue B, 62 ÷ 20 ≈ 3 {\displaystyle 62\div 20\approx 3} , then add the "tricky number" 3 {\displaystyle 3} to give 6 {\displaystyle 6} . The nearest cross street to 62 Avenue B is East 6th Street. If you are at 78 Riverside Drive, 78 ÷ 10 ≈ 8 {\displaystyle 78\div 10\approx 8} , then add the "tricky number" 72 {\displaystyle 72} to give 80 {\displaystyle 80} . The nearest cross street to 78 Riverside Drive is West 80th Street. If you are at 501 5th Avenue, 501 ÷ 20 ≈ 25 {\displaystyle 501\div 20\approx 25} , then add the "tricky number" 18 {\displaystyle 18} to give 43 {\displaystyle 43} . The nearest cross street to 501 5th Avenue is actually 42nd Street, not 43rd Street, as the Manhattan address algorithm only gives approximate answers.