iTools is a distributed infrastructure for managing, discovery, comparison and integration of computational biology resources. iTools employs Biositemap technology to retrieve and service meta-data about diverse bioinformatics data services, tools, and web-services. iTools is developed by the National Centers for Biomedical Computing as part of the NIH Road Map Initiative.
Concordancer
A concordancer is a computer program that automatically constructs a concordance—an alphabetised index of every occurrence of a word or phrase in a body of text, each entry displayed with its surrounding context. Concordancers are primary tools in corpus linguistics, lexicography, computer-assisted translation, and language teaching. The most common display format is the key word in context (KWIC) layout, in which each hit appears centred on a line with a fixed span of words to its left and right, enabling rapid scanning of usage patterns across many occurrences. == History == === Pre-computational concordances === The compilation of concordances predates computers by many centuries. Around 1230, the French Dominican cardinal Hugh of Saint-Cher directed a team of friars in assembling a concordance of the Latin Vulgate Bible, generally regarded as the first systematic concordance of any text. To help readers locate passages, Hugh divided each biblical chapter into lettered sections. Later milestones include a Hebrew Old Testament concordance compiled by Rabbi Mordecai Nathan (1448), Alexander Cruden's Complete Concordance to the Holy Scriptures (1737), and the manuscript Asaf ha-Mazkir, an unfinished concordance to the Babylonian Talmud compiled by Moses Rigotz around the turn of the 19th century. === First computer concordance === The first concordance produced with computing assistance was the Index Thomisticus, a comprehensive lexical index of the writings of and around Thomas Aquinas, totalling approximately 10.6 million Latin words. The Italian Jesuit priest Roberto Busa conceived the project in 1946 and secured the sponsorship of IBM in 1949 after a meeting with chairman Thomas J. Watson. Keypunch operators in Gallarate, Italy, encoded the texts onto punched cards from around 1950. IBM executive Paul Tasman developed the processing methods. The full 56-volume printed edition was completed around 1980, followed by a CD-ROM edition in 1989 and a web-accessible version in 2005. === The KWIC format === The key word in context (KWIC) display was formalised as a computational technique by Hans Peter Luhn, a researcher at IBM, in a 1960 paper in American Documentation. In KWIC output, each instance of the search term (the node word) is centred on a line with a fixed window of words to each side; sorting the resulting lines alphabetically by the immediately adjacent word reveals collocational and phraseological patterns at a glance. === COCOA === One of the first dedicated concordancing programs was COCOA (COunt and COncordance Generation on Atlas), created in 1965 by D. B. Russell at University College London and the Atlas Computer Laboratory in Harwell, Oxfordshire. Written in approximately 4,000 cards of FORTRAN, it processed text annotated with flat, non-hierarchical markup tags and could produce word counts and concordances in multiple languages. Within its first six months COCOA had been applied to texts in at least six languages. A second version designed for multiple mainframe platforms was distributed to British computing centres in the mid-1970s. Growing dissatisfaction with its interface and the eventual withdrawal of Atlas Laboratory support prompted British funding bodies to commission a successor program. === Oxford Concordance Program === The Oxford Concordance Program (OCP) was designed and written in FORTRAN by Susan Hockey and Ian Marriott at Oxford University Computing Services (OUCS) between 1979 and 1980 and first released in 1981. Hockey and Marriott acknowledged that OCP owed much to COCOA and the CLOC system at the University of Birmingham. OCP accepted COCOA-format markup to encode metadata such as author, act, scene, and line number, and was described by its authors as "a machine-independent text analysis program for producing word lists, indices and concordances in a variety of languages and alphabets." By the mid-1980s it had been licensed to approximately 240 institutions in 23 countries. A personal computer version, Micro-OCP, was developed for the IBM PC and sold by Oxford University Press from the late 1980s. Version 2 was rewritten in 1985–86 and documented in the same 1987 article by Hockey and co-author John Martin. === Personal computer era === The availability of affordable personal computers in the 1980s and 1990s enabled standalone concordancing applications that analysts could run locally without specialist computing facilities. MicroConcord, developed by Mike Scott and Tim Johns and published by Oxford University Press in 1993 for MS-DOS, was among the first concordancers designed specifically for classroom language teaching. WordSmith Tools, also developed by Mike Scott, was first released in 1996 and became one of the most widely used corpus analysis suites in academic linguistics research. Other tools from this era include TACT (University of Toronto, 1989), a suite of MS-DOS freeware programs for literary text analysis, and MonoConc, a Windows concordancer created by Michael Barlow. === Web-based concordancers === From the late 1990s onwards, web-based concordancers hosted on remote servers gave researchers browser access to large preloaded corpora without requiring local storage or processing. The Sketch Engine, developed by Adam Kilgarriff and Pavel Rychlý (Masaryk University), was launched commercially in July 2003 by Lexical Computing Limited and introduced word sketches—automatically generated one-page profiles of a word's typical grammatical relations and collocations. AntConc, created by Laurence Anthony at Waseda University, Tokyo, was first released in 2002 as freeware for Windows, macOS, and Linux. == Features == Modern concordancers typically offer a range of analytical functions beyond basic KWIC display. These commonly include: KWIC display with the node word centred and context words in aligned columns, sortable by the word one, two, or three positions to the left or right of the node (L1–L3 and R1–R3) Concordance plots, visualising the distribution of hits as marks along a scaled bar representing each text in the corpus Frequency and word lists, both alphabetical and ranked by frequency Collocation statistics, identifying words that co-occur with the search term more often than chance, quantified by measures such as mutual information, the t-score, or log-likelihood Keyword analysis, comparing word frequencies between a study corpus and a reference corpus to identify statistically distinctive items N-gram analysis, finding frequently recurring word sequences of a specified length Part-of-speech tagging integration, allowing searches filtered to particular grammatical categories Unicode support for multilingual text Bilingual and parallel concordancers additionally display aligned text in two or more languages side by side, enabling comparison of translation equivalents across language pairs. == Notable concordancers == === WordSmith Tools === Created by Mike Scott and first released in 1996, WordSmith Tools is a Windows corpus analysis suite that evolved from MicroConcord. Its three core modules are Concord (KWIC concordances), WordList (frequency and alphabetical word lists), and Keywords (statistical keyword identification relative to a reference corpus). Oxford University Press used WordSmith Tools for dictionary preparation work. Version 4.0 is freely available; later versions are sold by Lexical Analysis Software Limited. === AntConc === AntConc is a freeware, multiplatform concordancing toolkit created by Laurence Anthony, Professor of Applied Linguistics at Waseda University, Tokyo. First released in 2002 and formally described in a 2005 academic paper, it runs on Windows, macOS, and Linux. Its tools include a KWIC concordancer, a concordance plot for visualising distribution across texts, a collocates tool, a keyword list, and an n-gram analysis module. Because it is free and requires only plain text files, AntConc is widely used in linguistics courses and independent research worldwide. === Sketch Engine === The Sketch Engine is a corpus management and query system co-created by Adam Kilgarriff and Pavel Rychlý and launched in 2003 by Lexical Computing Limited. It provides browser-based access to over 800 corpora in more than 100 languages. Beyond concordance searching, it offers word sketches, collocation analysis, distributional thesaurus construction, keyword and terminology extraction, and diachronic analysis. It is used by major publishers including Macmillan and Oxford University Press for lexicographic research. A subset tool, SKELL (Sketch Engine for Language Learning), is freely accessible to individual learners. === Wmatrix === Wmatrix is a web-based corpus processing environment developed by Paul Rayson at the University Centre for Computer Corpus Research on Language (UCREL), Lancaster University. Alongside concordances and frequency lists, Wmatrix integrates CLAWS part-of-speech tagging and the USAS semantic tagger, enabling keyword analysis simultane
Color reproduction
Color reproduction is an aspect of color science concerned with producing light spectra that evoke a desired color, either through additive (light emitting) or subtractive (surface color) models. It converts physical correlates of color perception (CIE 1931 XYZ color space tristimulus values and related quantities) into light spectra that can be experienced by observers. In this way, it is the opposite of colorimetry. It is concerned with the faithful reproduction of a color in one medium, with a color in another, so it is a central concept in color management and relies heavily on color calibration. For example, food packaging must be able to faithfully reproduce the colors of the foods therein in order to appeal to a customer. This involves proper color calibration of at least four devices: Lighting, which must have a high color rendering index and not give a color cast to the object. Camera, which measures the reflected spectrum of the object and converts to a trichromatic color space (e.g. RGB). Screen, which reproduces color so a designer can proof the captured image and make color corrections as necessary. Printer, which reproduces the final color on paper.
Gerrit (software)
Gerrit ( GERR-it) is a free, web-based team code collaboration tool. Software developers in a team can review each other's modifications on their source code using a Web browser and approve or reject those changes. It integrates closely with Git, a distributed version control system. Gerrit is a fork of Rietveld, a code review tool for Subversion. Both are named after Dutch designer Gerrit Rietveld. == History == Originally written in Python like Rietveld, it is now written in Java (Java EE Servlet) with SQL since version 2 and a custom-made Git-based database (NoteDb) since version 3. In versions 2.0–2.16 Gerrit used Google Web Toolkit for its browser-based front-end. After being developed and used in parallel with GWT for versions 2.14–2.16, a new Polymer web UI replaced the GWT UI in version 3.0.
Radek Maneuver
The Radek Maneuver is a scale-up-then-scale-down tactic used in the administration of web services, specifically those deployed under a cloud computing paradigm (by a provider e.g. Amazon Elastic Compute Cloud or Microsoft Azure). == History == Developed by Olivier "Radek" Dabrowski in the mid-2010s, the Radek Maneuver was originally conceived of in using and maintaining applications running on a PaaS system. == Execution == The Radek Maneuver consists of a series of steps, usually executed via the PaaS or web portal interface. The tactic should be used when a service is misbehaving or otherwise experiencing errors, and the suspected cause is the underlying cloud layer, rather than the application layer. This includes networking issues and other "bad box" problems. The steps are as follows: Identify the application or service which is misbehaving. Increase the compute resource (number of CPU cores, amount of ram) for the instance on which the application is running. This is also known as scaling up. Wait for the application to re-deploy and stabilize. Scale back down to the original instance size. == Principle of action == This scale-up-scale-down method is understood to shift the application to a different physical machine underlying the PaaS service or application virtual machine. While this layer of the cloud computing stack is generally out of the access of an application developer (instead in the hands of the cloud provider), the maneuver allows troubleshooting and dodging errors in that layer.
Scene text
Scene text is text that appears in an image captured by a camera in an outdoor environment. The detection and recognition of scene text from camera captured images are computer vision tasks which became important after smart phones with good cameras became ubiquitous. The text in scene images varies in shape, font, colour and position. The recognition of scene text is further complicated sometimes by non-uniform illumination and focus. To improve scene text recognition, the International Conference on Document Analysis and Recognition (ICDAR) conducts a robust reading competition once in two years. The competition was held in 2003, 2005 and during every ICDAR conference. International association for pattern recognition (IAPR) has created a list of datasets as Reading systems. == Text detection == Text detection is the process of detecting the text present in the image, followed by surrounding it with a rectangular bounding box. Text detection can be carried out using image based techniques or frequency based techniques. In image based techniques, an image is segmented into multiple segments. Each segment is a connected component of pixels with similar characteristics. The statistical features of connected components are utilised to group them and form the text. Machine learning approaches such as support vector machine and convolutional neural networks are used to classify the components into text and non-text. In frequency based techniques, discrete Fourier transform (DFT) or discrete wavelet transform (DWT) are used to extract the high frequency coefficients. It is assumed that the text present in an image has high frequency components and selecting only the high frequency coefficients filters the text from the non-text regions in an image. == Word recognition == In word recognition, the text is assumed to be already detected and located and the rectangular bounding box containing the text is available. The word present in the bounding box needs to be recognized. The methods available to perform word recognition can be broadly classified into top-down and bottom-up approaches. In the top-down approaches, a set of words from a dictionary is used to identify which word suits the given image. Images are not segmented in most of these methods. Hence, the top-down approach is sometimes referred as segmentation free recognition. In the bottom-up approaches, the image is segmented into multiple components and the segmented image is passed through a recognition engine. Either an off the shelf Optical character recognition (OCR) engine or a custom-trained one is used to recognise the text.
Circular convolution
Circular convolution, also known as cyclic convolution, is a special case of periodic convolution, which is the convolution of two periodic functions that have the same period. Periodic convolution arises, for example, in the context of the discrete-time Fourier transform (DTFT). In particular, the DTFT of the product of two discrete sequences is the periodic convolution of the DTFTs of the individual sequences. And each DTFT is a periodic summation of a continuous Fourier transform function (see Discrete-time Fourier transform § Relation to Fourier Transform). Although DTFTs are usually continuous functions of frequency, the concepts of periodic and circular convolution are also directly applicable to discrete sequences of data. In that context, circular convolution plays an important role in maximizing the efficiency of a certain kind of common filtering operation. == Definitions == The periodic convolution of two T-periodic functions, h T ( t ) {\displaystyle h_{_{T}}(t)} and x T ( t ) {\displaystyle x_{_{T}}(t)} can be defined as: ∫ t o t o + T h T ( τ ) ⋅ x T ( t − τ ) d τ , {\displaystyle \int _{t_{o}}^{t_{o}+T}h_{_{T}}(\tau )\cdot x_{_{T}}(t-\tau )\,d\tau ,} where t o {\displaystyle t_{o}} is an arbitrary parameter. An alternative definition, in terms of the notation of normal linear or aperiodic convolution, follows from expressing h T ( t ) {\displaystyle h_{_{T}}(t)} and x T ( t ) {\displaystyle x_{_{T}}(t)} as periodic summations of aperiodic components h {\displaystyle h} and x {\displaystyle x} , i.e.: h T ( t ) ≜ ∑ k = − ∞ ∞ h ( t − k T ) = ∑ k = − ∞ ∞ h ( t + k T ) . {\displaystyle h_{_{T}}(t)\ \triangleq \ \sum _{k=-\infty }^{\infty }h(t-kT)=\sum _{k=-\infty }^{\infty }h(t+kT).} Then: Both forms can be called periodic convolution. The term circular convolution arises from the important special case of constraining the non-zero portions of both h {\displaystyle h} and x {\displaystyle x} to the interval [ 0 , T ] . {\displaystyle [0,T].} Then the periodic summation becomes a periodic extension, which can also be expressed as a circular function: x T ( t ) = x ( t m o d T ) , t ∈ R {\displaystyle x_{_{T}}(t)=x(t_{\mathrm {mod} \ T}),\quad t\in \mathbb {R} \,} (any real number) And the limits of integration reduce to the length of function h {\displaystyle h} : ( h ∗ x T ) ( t ) = ∫ 0 T h ( τ ) ⋅ x ( ( t − τ ) m o d T ) d τ . {\displaystyle (hx_{_{T}})(t)=\int _{0}^{T}h(\tau )\cdot x((t-\tau )_{\mathrm {mod} \ T})\ d\tau .} == Discrete sequences == Similarly, for discrete sequences, and a parameter N, we can write a circular convolution of aperiodic functions h {\displaystyle h} and x {\displaystyle x} as: ( h ∗ x N ) [ n ] ≜ ∑ m = − ∞ ∞ h [ m ] ⋅ x N [ n − m ] ⏟ ∑ k = − ∞ ∞ x [ n − m − k N ] {\displaystyle (hx_{_{N}})[n]\ \triangleq \ \sum _{m=-\infty }^{\infty }h[m]\cdot \underbrace {x_{_{N}}[n-m]} _{\sum _{k=-\infty }^{\infty }x[n-m-kN]}} This function is N-periodic. It has at most N unique values. For the special case that the non-zero extent of both x and h are ≤ N, it is reducible to matrix multiplication where the kernel of the integral transform is a circulant matrix. == Example == A case of great practical interest is illustrated in the figure. The duration of the x sequence is N (or less), and the duration of the h sequence is significantly less. Then many of the values of the circular convolution are identical to values of x∗h, which is actually the desired result when the h sequence is a finite impulse response (FIR) filter. Furthermore, the circular convolution is very efficient to compute, using a fast Fourier transform (FFT) algorithm and the circular convolution theorem. There are also methods for dealing with an x sequence that is longer than a practical value for N. The sequence is divided into segments (blocks) and processed piecewise. Then the filtered segments are carefully pieced back together. Edge effects are eliminated by overlapping either the input blocks or the output blocks. To help explain and compare the methods, we discuss them both in the context of an h sequence of length 201 and an FFT size of N = 1024. === Overlapping input blocks === This method uses a block size equal to the FFT size (1024). We describe it first in terms of normal or linear convolution. When a normal convolution is performed on each block, there are start-up and decay transients at the block edges, due to the filter latency (200-samples). Only 824 of the convolution outputs are unaffected by edge effects. The others are discarded, or simply not computed. That would cause gaps in the output if the input blocks are contiguous. The gaps are avoided by overlapping the input blocks by 200 samples. In a sense, 200 elements from each input block are "saved" and carried over to the next block. This method is referred to as overlap-save, although the method we describe next requires a similar "save" with the output samples. When an FFT is used to compute the 824 unaffected DFT samples, we don't have the option of not computing the affected samples, but the leading and trailing edge-effects are overlapped and added because of circular convolution. Consequently, the 1024-point inverse FFT (IFFT) output contains only 200 samples of edge effects (which are discarded) and the 824 unaffected samples (which are kept). To illustrate this, the fourth frame of the figure at right depicts a block that has been periodically (or "circularly") extended, and the fifth frame depicts the individual components of a linear convolution performed on the entire sequence. The edge effects are where the contributions from the extended blocks overlap the contributions from the original block. The last frame is the composite output, and the section colored green represents the unaffected portion. === Overlapping output blocks === This method is known as overlap-add. In our example, it uses contiguous input blocks of size 824 and pads each one with 200 zero-valued samples. Then it overlaps and adds the 1024-element output blocks. Nothing is discarded, but 200 values of each output block must be "saved" for the addition with the next block. Both methods advance only 824 samples per 1024-point IFFT, but overlap-save avoids the initial zero-padding and final addition.