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NHS COVID-19

NHS COVID-19 was a voluntary contact tracing app for monitoring the spread of the COVID-19 pandemic in England and Wales, in use from 24 September 2020 until 27 April 2023. It was available for Android and iOS smartphones, and could be used by anyone aged 16 or over. Two versions of the app were created. The first was commissioned by NHSX and developed by the Pivotal division of American software company VMware. A pilot deployment began in May 2020, but on 18 June development of the app was abandoned in favour of a second design using the Apple/Google Exposure Notification system. Scotland and Northern Ireland had separate contact tracing apps. A 2023 study estimated that in its first year of use, the app's contact tracing function prevented an estimated 1 million cases, and 9,600 deaths. == Description == The app allowed users to: See the alert level of their local authority area (in Wales) or information about restrictions (in England); to enable this, the user must enter the first half of their postcode "Check in" at places displaying an NHS QR code poster (no longer required by legislation after 26 January 2022, removed from the app the next month) Be notified when they have been in close contact with someone who has tested positive for the virus Be notified when local health protection teams determine that people with the virus had attended a business or other venue around the same time as the user Check their symptoms, and book a coronavirus test if necessary If asked to self-isolate, receive information and a daily "countdown". At first, "close contact" was defined as being within 2 metres for 15 minutes, or within 4 metres for a longer time. These time durations were reduced from 29 October 2020, to as little as three minutes when the other person is at their most infectious, i.e. soon after they begin showing symptoms. === Implementation === The Android app was coded in Kotlin, and the iOS app in Swift. The backend used Java and is deployed to Amazon Web Services using Terraform. The code of the app and back-end is open-source and available on GitHub. == Context == The app was part of the UK's test and trace programme which was chaired by Dido Harding; from 12 May 2020 Tom Riordan, chief executive of Leeds City Council, led the tracing effort. == First phase and cancellation == === Description === In March 2020, NHSX commissioned a contact tracing app to monitor the spread in the United Kingdom of the coronavirus disease 2019 (COVID-19) in the 2020 pandemic, developed by the Pivotal division of American software company VMware. The app used a centralised approach, in contrast to the Google / Apple contact tracing project. NHSX consulted ethicists and GCHQ's National Cyber Security Centre (NCSC) about the privacy aspects. The app recorded the make and model of the phone and asked the user for their postcode area. It generated a unique installation identification number and also a daily identification number. It then used Bluetooth Low Energy (BLE) to record the daily identification number of other users nearby. If a user was unwell, they could tell the app about symptoms which are characteristic of COVID-19, such as a fever and cough. These details were then passed to a central NHS server. This would assess the information and notify other users that have been in contact, giving them appropriate advice such as physical distancing. The NHS would also arrange for a swab test of the unwell user and the outcome would determine further notifications to contacts: if the test confirmed infection with COVID-19, the contacts would be asked to isolate. By June 2020, £11.8 million had been spent on the app; in 2020–21, £35 million was spent on the app. === Deployment === The first public trial of the app began on the Isle of Wight on 5 May 2020 and by 11 May it had been downloaded 55,000 times. When the first national contact tracing schemes were launched – Test, Trace, Protect in Wales on 13 May, then on 28 May NHS Test and Trace in England, and Test and Protect in Scotland – the app was not ready to be included. Replying to a question at the government's daily briefing on 8 June, Hancock was unable to give a date for rollout of the app in England, saying it would be brought in "when it's right to do so". On 17 June, Lord Bethell, junior minister for Innovation at the Department of Health and Social Care, said "we're seeking to get something going before the winter ... it isn't a priority for us at the moment". On 18 June, Health Secretary Matt Hancock announced development would switch to the Apple/Google system after admitting that Apple's restrictions on usage of Bluetooth prevented the app from working effectively. At the same press briefing Dido Harding, leader of the UK's test and trace programme, said "What we've done in really rigorously testing both our own Covid-19 app and the Google-Apple version is demonstrate that none of them are working sufficiently well enough to be actually reliable to determine whether any of us should self-isolate for two weeks [and] that's true across the world". === Concerns === The first, ultimately rejected, version of the app was subject to privacy concerns, the government backtracking on initial statements that the data collected from the app would not be shared outside the NHS. Matthew Gould, CEO of NHSX, the government department responsible for the app, said the data would be accessible to other organisations, but did not disclose which. Data collected would not necessarily be anonymised and would be held in a centralised repository. Over 150 of the UK's security and privacy experts warned the app's data could be used by 'a bad actor (state, private sector, or hacker)' to spy on citizens. Fears were discussed by the House of Commons' Human Rights Select Committee about plans for the app to record user location data. Parliament's Joint Committee on Human Rights said this version of the app should not be released without proper privacy protections. The second version of the app, released nationwide, addressed these concerns by employing a decentralised framework, the Apple/Google Exposure Notification system. Under this system, users remain pseudonymous: a person diagnosed with COVID-19 does not know which people are informed about an encounter, and contacted persons do not receive any information about the person diagnosed with COVID-19. The functionality of the app was also questioned in late April and early May 2020, as the software's use of Bluetooth required the app to be constantly running, meaning users could not use other apps or lock their device if the app was to function properly. The developers of the app were said to have found a way of working around this restriction. === Related contracts === Faculty – a company linked to Cambridge Analytica – provided research and modelling to NHSX in support of the response to the pandemic. Palantir, also linked to Cambridge Analytica, provided their data management platform. These contracts began in February and March respectively. == Second phase == As outlined on cancellation of the first app on 18 June 2020, the Department of Health and Social Care published on 30 July a brief description of the "next phase" app. Users would be able to scan a QR code at venues they visit, and later be notified if they had visited a place which was the source of a number of infections; the app would also assist with identifying symptoms and ordering a test. By using the Exposure Notification system from Apple and Google, personal data would be decentralised. Zuhlke Engineering Ltd, the UK branch of Swiss-based Zühlke Group, used 70 staff to complete the development of the app in 12 weeks. Zuhlke Engineering was awarded "Development Team of the Year" title at UK IT Industry awards in November 2021 for development of NHS COVID-19 application. === Timeline === Testing of the app by NHS volunteer responders, and selected residents of the Isle of Wight and the London Borough of Newham, began around 13 August. The app was made available to the public (aged 16 or over) in England and Wales on 24 September. An updated app released on 29 October, in part from collaboration with the Alan Turing Institute, improved the accuracy of measurements of the distance between the user's phone and other phones. At the same time, the duration threshold for determining exposure was reduced; this was expected to lead to an increase in the number of users told to self-isolate. An update to the app in April 2021, timed to coincide with easing of restrictions on hospitality businesses, was blocked by Apple and Google. It was intended that users who tested positive would be asked to share their history of visited venues, to assist in warning others, but this would have contravened assurances by Apple and Google that location data from devices would not be shared. === Statistics and effectiveness === The app was downloaded six million times on the first day it was generally availa
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Toolchain

A toolchain is a set of software development tools used to build and otherwise develop software. Often, the tools are executed sequentially and form a pipeline such that the output of one tool is the input for the next. Sometimes the term is used for a set of related tools that are not necessarily executed sequentially. A relatively common and simple toolchain consists of the tools to build for a particular operating system (OS) and CPU architecture: a compiler, a linker, and a debugger. With a cross-compiler, a toolchain can support cross-platform development. For building more complex software systems, many other tools may be in the toolchain. For example, for a video game, the toolchain may include tools for preparing sound effects, music, textures, 3-dimensional models and animations, and for combining these resources into the finished product.
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Web-based simulation

Web-based simulation (WBS) is the invocation of computer simulation services over the World Wide Web, specifically through a web browser. Increasingly, the web is being looked upon as an environment for providing modeling and simulation applications, and as such, is an emerging area of investigation within the simulation community. == Application == Web-based simulation is used in several contexts: In e-learning, various principles can quickly be illustrated to students by means of interactive computer animations, for example during lecture demonstrations and computer exercises. In distance learning, web-based simulation may provide an alternative to installing expensive simulation software on the student computer, or an alternative to expensive laboratory equipment. In software engineering, web-based emulation allows application development and testing on one platform for other target platforms, for example for various mobile operating systems or mobile web browsers, without the need of target hardware or locally installed emulation software. In online computer games, 3D environments can be simulated, and old home computers and video game consoles can be emulated, allowing the user to play old computer games in the web browser. In medical education, nurse education and allied health education (like sonographer training), web-based simulations can be used for learning and practicing clinical healthcare procedures. Web-based procedural simulations emphasize the cognitive elements such as the steps of the procedure, the decisions, the tools/devices to be used, and the correct anatomical location. == Client-side vs server-side approaches == Web-based simulation can take place either on the server side or on the client side. In server-side simulation, the numerical calculations and visualization (generation of plots and other computer graphics) is carried out on the web server, while the interactive graphical user interface (GUI) often partly is provided by the client-side, for example using server-side scripting such as PHP or CGI scripts, interactive services based on Ajax or a conventional application software remotely accessed through a VNC Java applet. In client-side simulation, the simulation program is downloaded from the server side but completely executed on the client side, for example using Java applets, Flash animations, JavaScript, or some mathematical software viewer plug-in. Server-side simulation is not scalable for many simultaneous users, but places fewer demands on the user computer performance and web-browser plug-ins than client-side simulation. The term on-line simulation sometimes refers to server-side web-based simulation, sometimes to symbiotic simulation, i.e. a simulation that interacts in real-time with a physical system. The upcoming cloud-computing technologies can be used for new server-side simulation approaches. For instance, there are multi-agent-simulation applications which are deployed on cloud-computing instances and act independently. This allows simulations to be highly scalable. == Existing tools == AgentSheets – graphically programmed tool for creating web-based The Sims-like simulation games, and for teaching beginner students programming. AnyLogic – a graphically programmed tool that generates Java code for discrete-event simulation, system dynamics and agent-based models Easy Java Simulations – a tool for modelling and visualization of physical phenomenons, that automatically generates Java code from mathematical expressions. ExploreLearning Gizmos – a large library of interactive online simulations for math and science education in grades 3–12. FreeFem++ Javascript Version – FreeFem++ is a free and open source PDE solver using the finite element method. GNU Octave web interfaces – MATLAB compatible open-source software Lanner Group Ltd L-SIM Server – Java-based discrete-event simulation engine which supports model standards such as BPMN 2.0 Nanohub – web 2.0 in-browser interactive simulation of nanotechnology NetLogo – a multi-agent programming language and integrated modeling environment that runs on the Java Virtual Machine OpenPlaG – PHP-based function graph plotter for the use on websites OpenEpi – web-based packet of tools for biostatistics Recursive Porous Agent Simulation Toolkit (Repast) – agent-based modeling and simulation toolkit implemented in Java and many other languages SageMath – open-source numerical-analysis software with web interface, based on the Python programming language SimScale – web-based simulation platform supporting computational fluid dynamics, solid mechanics, and thermodynamics StarLogo – agent-based simulation language written in Java. VisSim viewer – graphically programmed data-flow diagrams for simulation of dynamical systems webMathematica and Mathematica Player – a computer algebra system and programming language. VisualSim Architect – VisualSim Explorer enables system-level models to be embedded in documents for viewing, simulation and analysis from within a web browser without any local software installation.
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Cryptee

Cryptee is a privacy focused client-side encrypted and cross-platform productivity suite and data storage service. == History == Cryptee was founded in 2017, by John Ozbay, a cybersecurity researcher, commenter, and activist, to exclusively focus on providing a secure document editing service similar to Google Docs and Photos for everyone, with a particular focus on victims and survivors of domestic abuse, journalists and reporters. == Software == Users can write personal documents, notes, journals, store images, videos, and various kinds of other files. The source code of Cryptee is open source and publicly available to allow anyone to audit the service with ease, and help identify errors or potential vulnerabilities in a public and transparent manner. Cryptee has a few key features that differentiate it from other services in the industry, such as its Ghost Folders and Ghost Albums features, built specifically with victims and survivors of domestic abuse, journalists and reporters in mind. Cryptee allows users to hide (ghost) folders for plausible deniability also as known as deniable encryption in the field of cryptography and steganography, and ensure privacy even under coercion. === Features === Cryptee Docs' features include: To-do lists, Markdown support, KaTeX math and file attachments. cross-platform accessible, as it is a progressive web app. Bulk transfer from other note taking apps such as Evernote. Encrypted PDF and print-accurate (A4 and U.S. Letter paper-sized) text editing. Ability to edit docx files Cryptee Photos' features include: Ability to create slideshows. Ability to store original quality of photos. Ability to tag photos for organization. === Commercial strategy === The company's commercial strategy is focused on offering to its users an open source and transparent Photo Storage, Document Editor and Cloud Storage services without trackers or advertisements as it seeks to compete with Google Docs, Google Photos and similar services through its offerings. === Privacy === Cryptee utilizes zero-access storage to safe-keep all users' sensitive digital belongings. == Advocacy == === Lockdown mode === In July 2022, to fortify iPhones against the Pegasus Spyware, Apple announced a new, upcoming Lockdown Mode feature in iOS 16, welcomed by many experts. In the following weeks after Apple's announcement, in August 2022, the Founder and CEO of Cryptee, and privacy activist John Ozbay published their research detailing shortcoming of Apple's Lockdown Mode. They demonstrated that enabling Lockdown Mode makes it possible for all websites and online ads to be able to detect if users have Lockdown Mode enabled or not. This was due to the fact that disabling web fonts (an attack surface) was detectable by websites. === Confrontations against Apple === ==== On PWAs ==== In February 2024, Apple announced plans to kill progressive web apps on iOS devices in the EU, claiming it was to comply with the Digital Markets Act (DMA). The announcement was criticized as anti-competitive by many in the tech industry, including by Tim Sweeney, the CEO of Epic Games. In response, Cryptee started working together with Open Web Advocacy (OWA), an international not-for-profit digital rights group to advocate for the future of the open web, promote web browser choice on mobile operating systems through challenging Apple's anti-competitive third party browser engine ban, and to champion the use and equality of progressive web apps over native apps, by reaching out to the European Union's Digital Markets Act (DMA) team. To better understand the consequences of Apple's decision to kill web apps, the EU announced that they "seek to investigate Apple over cutting off web apps", and that they sent "requests for information to Apple and to app developers, who can provide useful information for our assessment". Apart from sending a response to the EU, Cryptee, along with the OWA, launched an open letter to Tim Cook, which in 48 hours, got thousands of signatories including European Parliament Members Karen Melchior and Patrick Breyer; and thousands of other developers and organizations from over 100 countries. Consequently, 24 hours later, Apple backed off, and reversed course on its plan to cut off progressive web apps in the EU. ==== Ozbay's representations ==== Following the events, eventually on March 18, 2024, Founder and CEO of Cryptee John Ozbay represented the Open Web Advocacy group in European Union's Digital Markets Act (DMA) hearing for Apple. At the hearing, OWA confronted Apple, accused Apple of "maliciously intending to undermine user choice", and stated that there was no defense for Apple's behavior. In response, according to the tech news outlet Ars Technica, Apple's spokesperson "seemed to dodge Ozbay's question". ==== Cooperation with the EU ==== Within a week of the hearing, the European Union announced a DMA non-compliance investigation against Apple and United States' Department of Justice filed an antitrust lawsuit against Apple. A few months later, on June 27, 2024, Cryptee, in cooperation with EDRi — an international advocacy group, along with Article 19 — a British international human rights organization, Privacy International, F-Droid, Free Software Foundation Europe, Guardian Project and others have submitted a comprehensive analysis to the European Commission about how Apple's plans to comply with the Digital Markets Act are insufficient. == Reviews == In a 2018 article, Wall Street Journal's MarketWatch reviewed Cryptee, articulating the fact that Cryptee offers zero-access storage for photos, files, documents and notes, and pointed out that: "Being based in Estonia puts Cryptee outside the “14 eyes jurisdiction,” an international surveillance alliance of European Union and North American countries, making it less likely it will be targeted with demands for data". In addition, the review highlighted Cryptee's Ghost Folders feature which ensures privacy even under coercion. In a 2019 article, Reclaim The Net named Cryptee as one of the "5 great privacy-focused Evernote alternatives to keep your notes safe", underlining that: "When it comes to security, this app is state of the art." and that "When making this app, the developers thought about every aspect of security and have taken every precaution to make it as secure as possible.". The review further underscored Cryptee's open-source nature, its strong encryption, and easy migration features. In a 2021 article, The Verge reviewed Cryptee, pointing out that Cryptee, based out of Europe, is one of the main photo storage service alternatives to Google Photos, and that it's their recommendation for users who are "concerned about privacy and like the idea of encryption" as Cryptee "offers to keep all your photos encrypted using AES-256". In a 2024 article, Beebom, enlisted Cryptee as one of the "7 best iCloud Photos Alternatives for iPhone and iPad", complimenting Cryptee's simplicity, its use of encryption to safeguard users' photos against hacking by not storing any unencrypted data. The article also provided further attention to Cryptee's additional features such as such as Ghost Albums, slideshows, easy-to-use drag and drop uploads, tagging and users' ability to store original-quality photos on Cryptee, concluding that Cryptee is "a safe bet if you are on the lookout for a privacy-centric iCloud Photos alternative".
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Audio inpainting

Audio inpainting (also known as audio interpolation) is an audio restoration task which deals with the reconstruction of missing or corrupted portions of a digital audio signal. Inpainting techniques are employed when parts of the audio have been lost due to various factors such as transmission errors, data corruption or errors during recording. The goal of audio inpainting is to fill in the gaps (i.e., the missing portions) in the audio signal seamlessly, making the reconstructed portions indistinguishable from the original content and avoiding the introduction of audible distortions or alterations. Many techniques have been proposed to solve the audio inpainting problem and this is usually achieved by analyzing the temporal and spectral information surrounding each missing portion of the considered audio signal. Classic methods employ statistical models or digital signal processing algorithms to predict and synthesize the missing or damaged sections. Recent solutions, instead, take advantage of deep learning models, thanks to the growing trend of exploiting data-driven methods in the context of audio restoration. Depending on the extent of the lost information, the inpainting task can be divided in three categories. Short inpainting refers to the reconstruction of few milliseconds (approximately less than 10) of missing signal, that occurs in the case of short distortions such as clicks or clipping. In this case, the goal of the reconstruction is to recover the lost information exactly. In long inpainting instead, with gaps in the order of hundreds of milliseconds or even seconds, this goal becomes unrealistic, since restoration techniques cannot rely on local information. Therefore, besides providing a coherent reconstruction, the algorithms need to generate new information that has to be semantically compatible with the surrounding context (i.e., the audio signal surrounding the gaps). The case of medium duration gaps lays between short and long inpainting. It refers to the reconstruction of tens of millisecond of missing data, a scale where the non-stationary characteristic of audio already becomes important. == Definition == Consider a digital audio signal x {\displaystyle \mathbf {x} } . A corrupted version of x {\displaystyle \mathbf {x} } , which is the audio signal presenting missing gaps to be reconstructed, can be defined as x ~ = m ∘ x {\displaystyle \mathbf {\tilde {x}} =\mathbf {m} \circ \mathbf {x} } , where m {\displaystyle \mathbf {m} } is a binary mask encoding the reliable or missing samples of x {\displaystyle \mathbf {x} } , and ∘ {\displaystyle \circ } represents the element-wise product. Audio inpainting aims at finding x ^ {\displaystyle \mathbf {\hat {x}} } (i.e., the reconstruction), which is an estimation of x {\displaystyle \mathbf {x} } . This is an ill-posed inverse problem, which is characterized by a non-unique set of solutions. For this reason, similarly to the formulation used for the inpainting problem in other domains, the reconstructed audio signal can be found through an optimization problem that is formally expressed as x ^ ∗ = argmin X ^ L ( m ∘ x ^ , x ~ ) + R ( x ^ ) {\displaystyle \mathbf {\hat {x}} ^{}={\underset {\hat {\mathbf {X} }}{\text{argmin}}}~L(\mathbf {m} \circ \mathbf {\hat {x}} ,\mathbf {\tilde {x}} )+R(\mathbf {\hat {x}} )} . In particular, x ^ ∗ {\displaystyle \mathbf {\hat {x}} ^{}} is the optimal reconstructed audio signal and L {\displaystyle L} is a distance measure term that computes the reconstruction accuracy between the corrupted audio signal and the estimated one. For example, this term can be expressed with a mean squared error or similar metrics. Since L {\displaystyle L} is computed only on the reliable frames, there are many solutions that can minimize L ( m ∘ x ^ , x ~ ) {\displaystyle L(\mathbf {m} \circ \mathbf {\hat {x}} ,\mathbf {\tilde {x}} )} . It is thus necessary to add a constraint to the minimization, in order to restrict the results only to the valid solutions. This is expressed through the regularization term R {\displaystyle R} that is computed on the reconstructed audio signal x ^ {\displaystyle \mathbf {\hat {x}} } . This term encodes some kind of a-priori information on the audio data. For example, R {\displaystyle R} can express assumptions on the stationarity of the signal, on the sparsity of its representation or can be learned from data. == Techniques == There exist various techniques to perform audio inpainting. These can vary significantly, influenced by factors such as the specific application requirements, the length of the gaps and the available data. In the literature, these techniques are broadly divided in model-based techniques (sometimes also referred as signal processing techniques) and data-driven techniques. === Model-based techniques === Model-based techniques involve the exploitation of mathematical models or assumptions about the underlying structure of the audio signal. These models can be based on prior knowledge of the audio content or statistical properties observed in the data. By leveraging these models, missing or corrupted portions of the audio signal can be inferred or estimated. An example of a model-based techniques are autoregressive models. These methods interpolate or extrapolate the missing samples based on the neighboring values, by using mathematical functions to approximate the missing data. In particular, in autoregressive models the missing samples are completed through linear prediction. The autoregressive coefficients necessary for this prediction are learned from the surrounding audio data, specifically from the data adjacent to each gap. Some more recent techniques approach audio inpainting by representing audio signals as sparse linear combinations of a limited number of basis functions (as for example in the Short Time Fourier Transform). In this context, the aim is to find the sparse representation of the missing section of the signal that most accurately matches the surrounding, unaffected signal. The aforementioned methods exhibit optimal performance when applied to filling in relatively short gaps, lasting only a few tens of milliseconds, and thus they can be included in the context of short inpainting. However, these signal-processing techniques tend to struggle when dealing with longer gaps. The reason behind this limitation lies in the violation of the stationarity condition, as the signal often undergoes significant changes after the gap, making it substantially different from the signal preceding the gap. As a way to overcome these limitations, some approaches add strong assumptions also about the fundamental structure of the gap itself, exploiting sinusoidal modeling or similarity graphs to perform inpainting of longer missing portions of audio signals. === Data-driven techniques === Data-driven techniques rely on the analysis and exploitation of the available audio data. These techniques often employ deep learning algorithms that learn patterns and relationships directly from the provided data. They involve training models on large datasets of audio examples, allowing them to capture the statistical regularities present in the audio signals. Once trained, these models can be used to generate missing portions of the audio signal based on the learned representations, without being restricted by stationarity assumptions. Data-driven techniques also offer the advantage of adaptability and flexibility, as they can learn from diverse audio datasets and potentially handle complex inpainting scenarios. As of today, such techniques constitute the state-of-the-art of audio inpainting, being able to reconstruct gaps of hundreds of milliseconds or even seconds. These performances are made possible by the use of generative models that have the capability to generate novel content to fill in the missing portions. For example, generative adversarial networks, which are the state-of-the-art of generative models in many areas, rely on two competing neural networks trained simultaneously in a two-player minmax game: the generator produces new data from samples of a random variable, the discriminator attempts to distinguish between generated and real data. During the training, the generator's objective is to fool the discriminator, while the discriminator attempts to learn to better classify real and fake data. In GAN-based inpainting methods the generator acts as a context encoder and produces a plausible completion for the gap only given the available information surrounding it. The discriminator is used to train the generator and tests the consistency of the produced inpainted audio. Recently, also diffusion models have established themselves as the state-of-the-art of generative models in many fields, often beating even GAN-based solutions. For this reason they have also been used to solve the audio inpainting problem, obtaining valid results. These models generate new data instances by inverting the
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BioBIKE

BioBike(nee. BioLingua ) is a cloud-based, through-the-web programmable (Paas) symbolic biocomputing and bioinformatics platform that aims to make computational biology, and especially intelligent biocomputing (that is, the application of Artificial Intelligence to computational biology) accessible to research scientists who are not expert programmers. == Unique capabilities == BioBIKE is an integrated symbolic biocomputing and bioinformatics platform, built from the start as an entirely (what is now called) cloud-based architecture where all computing is done in remote servers, and all user access is accomplished through web browsers. BioBIKE has a built-in frame system in which all objects, data, and knowledge are represented. This enables code written either in the native Lisp, in the visual programming language, or systems of rules expressed in the SNARK theorem prover to access the whole of biological knowledge in an integrated manner. For its time (released in 2002) it was unique in permitting users to create fully functional biocomputing programs that run on the back-end servers entirely through the web browser UI. (In modern terms it was one of the first PaaS (Platform as a Service) systems, predating even Salesforce in this capability.) Initially this programming was carried out in raw Lisp, but Jeff Elhai's team at VCU, with NSF funding, created an entirely graphical programming environment on top of BioBIKE based upon the Boxer-style programming environments. Being a multi-headed, multi-threaded, multi-user, multi-tenancy cloud-based system, BioBIKE users were able to directly work together through their web browsers, remotely sharing the same listener and memory space. This permitted a unique sort of collaboration, discussed in Shrager (2007). A specialized offshoot of BioBIKE called "BioDeducta" includes SRI's SNARK theorem prover, offering unique "deductive biocomputing" capabilities. == Implementation == BioBIKE is open-source software implemented using the Lisp programming language. Continuing development takes place by the BioBIKE team centered at Virginia Commonwealth University . == History == BioBIKE was originally called "BioLingua", and was developed by Jeff Shrager at The Carnegie Inst. of Washington Dept. of Plant Biology, and JP Massar with funding from NASA's Astrobiology Division. Shrager and Massar wanted to create a web-based, multi-user Lisp Machine, specialized for bioinformatics. Other early contributors to the project included Mike Travers, and Jeff Elhai of VCU. Elhai obtained continuing funding from the National Science Foundation for the project, which was renamed BioBIKE. Elhai and colleagues added BioBIKE's unique visual programming language. Shrager, meanwhile, collaborated with Richard Waldinger at SRI to build SRI's (SNARK) theorem prover into BioBIKE, creating a deductive biocomputing system, called BioDeducta. == Instances == There used to be a number of BioBIKE verticals in different biological domains, including viral pathogens, cyanobacteria and other bacteria, Arabidopsis thaliana, and several others described in the references.
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Toad (software)

Toad is a database management toolset from Quest Software for managing relational and non-relational databases using SQL aimed at database developers, database administrators, and data analysts. The Toad toolset runs against Oracle, SQL Server, IBM DB2 (LUW & z/OS), SAP and MySQL. A Toad product for data preparation supports many data platforms. == History == A practicing Oracle DBA, Jim McDaniel, designed Toad for his own use in the mid-1990s. He called it Tool for Oracle Application Developers, shortened to "TOAD". McDaniel initially distributed the tool as shareware and later online as freeware. Quest Software acquired TOAD in October 1998. Quest Software itself was acquired by Dell in 2012 to form Dell Software. In June 2016, Dell announced the sale of their software division, including the Quest business, to Francisco Partners and Elliott Management Corporation. On October 31, 2016, the sale was finalized. On November 1, 2016, the sale of Dell Software to Francisco Partners and Elliott Management was completed, and the company re-launched as Quest Software. == Features == Connection Manager - Allow users to connect natively to the vendor’s database whether on-premise or DBaaS. Browser - Allow users to browse all the different database/schema objects and their properties effective management. Editor - A way to create and maintain scripts and database code with debugging and integration with source control. Unit Testing (Oracle) - Ensures code is functionally tested before it is released into production. Static code review (Oracle) - Ensures code meets required quality level using a rules-based system. SQL Optimization - Provides developers with a way to tune and optimize SQL statements and database code without relying on a DBA. Advanced optimization enables DBAs to tune SQL effectively in production. Scalability testing and database workload replay - Ensures that database code and SQL will scale properly before it gets released into production. == Books == Toad Pocket Reference for Oracle plsql 1st Edition by Jim McDaniel and Patrick McGrath, O'Reilly, 2002 (ISBN 0596003374, ISBN 978-0-596-00337-1) Toad Pocket Reference for Oracle 2nd Edition by Jeff Smith, Bert Scalzo, and Patrick McGrath, O'Reilly, 2005 (ISBN 0596009712, ISBN 978-0-596-00971-7) TOAD Handbook by Bert Scalzo and Dan Hotka, Sams, 2003 (ISBN 0672324865, ISBN 978-0-672-32486-4) TOAD Handbook 2nd Edition by Bert Scalzo and Dan Hotka, Addison-Wesley Professional, 2009 (ISBN 0321649109, ISBN 978-0-321-64910-2). TOAD Handbook 2nd Edition by Bert Scalzo and Dan Hotka, Addison-Wesley Professional, 2009 (ISBN 0321649109, ISBN 978-0-321-64910-2).
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Software component

A software component is a modular unit of software that encapsulates specific functionality. The desired characteristics of a component are reusability and maintainability. == Value == Components allow software developers to assemble software with reliable parts rather than writing code for every aspect. It makes implementation more like factory assembly than custom building. == Attributes == Desirable attributes of a component include but are not limited to: Cohesive – encapsulates related functionality Reusable Robust Substitutable – can be replaced by another component with the same interface Documented Tested == Third-party == Some components are built in-house by the same organization or team building the software system. Some are third-party, developed elsewhere and assembled into the software system. == Component-based software engineering == For large-scale systems, component-based development encourages a disciplined process to manage complexity. == Framework == Some components conform to a framework technology that allows them to be consumed in a well-known way. Examples include: CORBA, COM, Enterprise JavaBeans, and the .NET Framework. == Modeling == Component design is often modeled visually. In Unified Modeling Language (UML) 2.0 a component is shown as a rectangle, and an interface is shown as a lollipop to indicate a provided interface and as a socket to indicate consumption of an interface. == History == The idea of reusable software components was promoted by Douglas McIlroy in his presentation at the NATO Software Engineering Conference of 1968. (One goal of that conference was to resolve the so-called software crisis of the time.) In the 1970s, McIlroy put this idea into practice with the addition of the pipeline feature to the Unix operating system. Brad Cox refined the concept of a software component in the 1980s. He attempted to create an infrastructure and market for reusable third-party components by inventing the Objective-C programming language. IBM introduced System Object Model (SOM) in the early 1990s. Microsoft introduced Component Object Model (COM) in the early 1990s. Microsoft built many domain-specific component technologies on COM, including Distributed Component Object Model (DCOM), Object Linking and Embedding (OLE), and ActiveX.
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Opponent process

The opponent process is a hypothesis of color vision that states that the human visual system interprets information about color by processing signals from the three types of photoreceptor cells in an antagonistic manner. The three types of cones are called L, M, and S. The names stand for "Long wavelength sensitive,” "middle wavelength sensitive," and "short wavelength sensitive." The opponent-process theory implicates three opponent channels: L versus M, S versus (L+M), and a luminance channel (+ versus -). These cone-opponent mechanisms were at one time thought to be the neural substrate for a psychological theory called Hering's Opponent Colors Theory, which calls for three psychologically important opponent color processes: red versus green, blue versus yellow, and black versus white (luminance). The Opponent Colors Theory is named for the German physiologist Ewald Hering who proposed the idea in the late 19th century. However, it has been argued that Hering’s Opponent Colors Theory lacks adequate phenomenological and empirical support, and may not be a necessary feature of normal human color experience. Correspondingly, considerable physiological and behavioral evidence proves that the physiological cone opponent mechanisms do not constitute the neurobiological basis for Hering's Opponent Colors Theory. == Color theory == === Complementary colors === When staring at a bright color for a while (e.g. red), then looking away at a white field, an afterimage is perceived, such that the original color will evoke its complementary color (cyan, in the case of red input). When complementary colors are combined or mixed, they "cancel each other out" and become neutral (white or gray). That is, complementary colors are never perceived as a mixture; there is no "greenish red" or "yellowish blue", despite claims to the contrary. The strongest color contrast that a color can have is its complementary color. Complementary colors may also be called "opposite colors" and they were originally considered the primary evidence in support of Hering's Opponent Colors Theory. There are two fatal problems with this evidence. First, the complement of red is not green, as called for by Hering's theory; it is bluish-green. And second, there exists a complementary color for every color, so there is nothing special about the set of complementary pairs picked out by Hering's theory. === Unique hues === The colors that define the extremes for each opponent channel are called unique hues, as opposed to composite (mixed) hues. Ewald Hering first defined the unique hues as red, green, blue, and yellow, and based them on the concept that these colors could not be simultaneously perceived. For example, a color cannot appear both red and green. These definitions have been experimentally refined and are represented today by average hue angles of 353° (carmine red), 128° (cobalt green), 228° (cobalt blue), 58° (yellow). The unique hues are a defining feature of many psychological color spaces, but there is substantial evidence showing that the unique hues are not hard wired in the nervous system, contrary to the stipulations of Hering's Opponent Colors Theory. Unique hues can differ between individuals and are often used in psychophysical research to measure variations in color perception due to color-vision deficiencies or color adaptation. While there is considerable inter-subject variability when defining unique hues experimentally, an individual's unique hues are very consistent, to within a few nanometers of wavelength. == Physiological basis == === Relation to LMS color space === The trichromatic theory is in conflict with Hering's Opponent Colors Theory, although it is compatible with a physiological opponent process that compares the outputs of the different classes of cone types. The poles of these cone opponent mechanisms do not correspond to the unique hues of Hering's Opponent Colors Theory and unlike the unique hues, have no privilege in color perception. Most humans have three different cone cells in their retinas that facilitate trichromatic color vision. Colors are determined by the proportional excitation of these three cone types, i.e. their quantum catch. The levels of excitation of each cone type are the parameters that define LMS color space. To calculate the opponent process tristimulus values from the LMS color space, the cone excitations must be compared: The luminous (achromatic) opponent channel is a weighted sum of all three cone cells (plus the rod cells in some conditions). The red–green opponent channel is equal to the difference of the L- and M-cones. The blue–yellow opponent channel is equal to the difference of the S-cone and the average/weighted sum of the L- and M-cones. Most mammals have no L cone (the primate L cone arose from a gene duplication of the M cone opsin gene). These mammals still show two kinds of opponent channels in their retinal ganglion cells: the achromatic channel and the blue-yellow opponency channel. === Cone opponent mechanisms are encoded in the retina === The output of different types of cones are compared by cells in the retina including retina bipolar cells (which compare signals from L and M cones) and bistratified retinal ganglion cells (which compare S cone signals with L and M cone signals). The output of bipolar cells is relayed to the visual cortex by the retinal ganglion cells (RGCs) by way of a thalamic relay station called the lateral geniculate nucleus (LGN) of the thalamus. Much of the scientific knowledge of retinal ganglion cell physiology was obtained by neural recordings of cells in the LGN. The cone-opponent mechanisms in the retina and LGN represent a fundamental physiological opponent process but do not represent the unique hues (or Hering's Opponent Colors Theory). For example, the colors that best elicit responses of the bistratified S-(L+M)-opponent neurons are best described as purplish (or lavender) and lime-green, not "blue" and "yellow". The neurons are sometimes referred to as "blue–yellow" neurons, but this is a historical artifact dating to the time when it was thought that Hering's Opponent Colors Theory was hardwired by the retina and the mismatch between the colors to which they are optimally tuned and Hering's Opponent Colors was overlooked. Cone opponent mechanisms exist in the retinas of many mammals, including monkeys, mice, and cats. In primates, the LGN contains three major classes of layers: Magnocellular layers (M, large-cell) – responsible largely for the luminance channel Parvocellular layers (P, small-cell) – responsible largely for red–green opponency Koniocellular layers (K) – responsible largely for blue–yellow opponency, poor spatial resolution, long latency Other mammals such as cats also have three cell types denoted as X (magno), Y (parvo), and W (konio). The W type is beyond most doubt homologous to the primate K type. There are some subtle differences between the M and X types as well as the Y and P types to make the correspondence unclear. === Advantage === Transmitting information in opponent-channel color space could be advantageous over transmitting it in LMS color space ("raw" signals from each cone type). There is some overlap in the wavelengths of light to which the three types of cones (L for long-wave, M for medium-wave, and S for short-wave light) respond, so it is more efficient for the visual system (from a perspective of dynamic range) to record differences between the responses of cones, rather than each type of cone's individual response. Hurvich and Jameson argued that the use of opponent-channel color space would increase color contrast, making the information easier to process by later stages of vision. === Color blindness === Color blindness can be classified by the cone cell that is affected (protan, deutan, tritan) or by the opponent channel that is affected (red–green or blue–yellow). In either case, the channel can either be inactive (in the case of dichromacy) or have a lower dynamic range (in the case of anomalous trichromacy). For example, individuals with deuteranopia see little difference between the red and green unique hues. == History == Johann Wolfgang von Goethe first studied the physiological effect of opposed colors in his Theory of Colours in 1810. Goethe arranged his color wheel symmetrically "for the colours diametrically opposed to each other in this diagram are those which reciprocally evoke each other in the eye. Thus, yellow demands purple; orange, blue; red, green; and vice versa: Thus again all intermediate gradations reciprocally evoke each other." Ewald Hering proposed opponent color theory in 1892. He thought that the colors red, yellow, green, and blue are special in that any other color can be described as a mix of them, and that they exist in opposite pairs. That is, either red or green is perceived and never greenish-red: Even though yellow is a mixture of red and green in the RGB color theory, humans
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Endomondo

Endomondo is a health and wellness website. It allows users to track their health statistics and provides insights on fitness trends. Originally launched in 2007, Endomondo was acquired by Under Armour in 2015. Under Armour shut down Endomondo in 2020, but, by 2024, Endomondo re-launched as its own entity. == History == Endomondo started in Denmark in 2007 by Mette Lykke, Christian Birk and Jakob Nordenhof Jønck. In 2011, the company opened an office in Silicon Valley, USA, but kept its research and development department in Denmark. In 2013, Endomondo LLC was listed in Red Herring as a European finalists for promising start-ups. The same year, Christian Birk and Jakob Nordenhof Jønck left the daily operation of the company, but kept co-ownership. In February 2015, Endomondo LLC was acquired by athletic apparel maker Under Armour for $85 million. Endomondo, at that time, had over 20 million users. In October 2020, Under Armour announced that Endomondo would be shutting down and selling off MyFitnessPal to the private equity firm Francisco Partners for $345 million. Service stopped on 31 December 2020, giving customers until 15 February 2021 to download an archive of their historic data. In 2024, Endomondo.com was brought back online as a professional fitness guidance website. == Features == Endomondo provides numerous workouts, guidance on exercises, performance-enhancing nutrition, and tips. Previously, Endomondo was able to track numerous fitness attributes such as running routes, distance, duration, and calories. The software helped analyze performance and recommend improvements. There was a free and a paid version available of Endomondo. The free version had advertisements. The paid Premium version was free of advertisements and included additional features such as the possibility to create one's own training plan. The offering of additional features was different between the Android, IOS and Windows platforms, and had significantly better features for tracking performance over time than UnderArmours suggested replacement. Endomondo offered challenges of various types to the user and allowed users to create their own challenges.
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Clara.io

Clara.io is web-based freemium 3D computer graphics software developed by Exocortex, a Canadian software company. The free or "Basic" component of their freemium offering, however, places severe restrictions, such as on saving models and importing texture maps, which are undisclosed in the company's own descriptions of their plans.vf TMN == History == Clara.io was announced in July 2013, and first presented as part of the official SIGGRAPH 2013 program later that month. By November 2013, when the open beta period started, Clara.io had 14,000 registered users. Clara.io claimed to have 26,000 registered users in January 2014, which grew to 85,000 by December 2014. Clara.io was permanently shut down on December 31, 2022, but the site is currently still partially functional to logged-in users. == Features == Polygonal modeling Constructive solid geometry Key frame animation Skeletal animation Hierarchical scene graph Texture mapping Photorealistic rendering (streaming cloud rendering using V-Ray Cloud) Scene publishing via HTML iframe embedding FBX, Collada, OBJ, STL and Three.js import/export Collaborative real-time editing Revision control (versioning & history) Scripting, Plugins & REST APIs 3D model library Unlisted and Private scenes (paid subscriptions only). == Technology == Clara.io is developed using HTML5, JavaScript, WebGL and Three.js. Clara.io does not rely on any browser plugins and thus runs on any platform that has a modern standards compliant browser. == Screenshots ==
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Web-based simulation

Web-based simulation (WBS) is the invocation of computer simulation services over the World Wide Web, specifically through a web browser. Increasingly, the web is being looked upon as an environment for providing modeling and simulation applications, and as such, is an emerging area of investigation within the simulation community. == Application == Web-based simulation is used in several contexts: In e-learning, various principles can quickly be illustrated to students by means of interactive computer animations, for example during lecture demonstrations and computer exercises. In distance learning, web-based simulation may provide an alternative to installing expensive simulation software on the student computer, or an alternative to expensive laboratory equipment. In software engineering, web-based emulation allows application development and testing on one platform for other target platforms, for example for various mobile operating systems or mobile web browsers, without the need of target hardware or locally installed emulation software. In online computer games, 3D environments can be simulated, and old home computers and video game consoles can be emulated, allowing the user to play old computer games in the web browser. In medical education, nurse education and allied health education (like sonographer training), web-based simulations can be used for learning and practicing clinical healthcare procedures. Web-based procedural simulations emphasize the cognitive elements such as the steps of the procedure, the decisions, the tools/devices to be used, and the correct anatomical location. == Client-side vs server-side approaches == Web-based simulation can take place either on the server side or on the client side. In server-side simulation, the numerical calculations and visualization (generation of plots and other computer graphics) is carried out on the web server, while the interactive graphical user interface (GUI) often partly is provided by the client-side, for example using server-side scripting such as PHP or CGI scripts, interactive services based on Ajax or a conventional application software remotely accessed through a VNC Java applet. In client-side simulation, the simulation program is downloaded from the server side but completely executed on the client side, for example using Java applets, Flash animations, JavaScript, or some mathematical software viewer plug-in. Server-side simulation is not scalable for many simultaneous users, but places fewer demands on the user computer performance and web-browser plug-ins than client-side simulation. The term on-line simulation sometimes refers to server-side web-based simulation, sometimes to symbiotic simulation, i.e. a simulation that interacts in real-time with a physical system. The upcoming cloud-computing technologies can be used for new server-side simulation approaches. For instance, there are multi-agent-simulation applications which are deployed on cloud-computing instances and act independently. This allows simulations to be highly scalable. == Existing tools == AgentSheets – graphically programmed tool for creating web-based The Sims-like simulation games, and for teaching beginner students programming. AnyLogic – a graphically programmed tool that generates Java code for discrete-event simulation, system dynamics and agent-based models Easy Java Simulations – a tool for modelling and visualization of physical phenomenons, that automatically generates Java code from mathematical expressions. ExploreLearning Gizmos – a large library of interactive online simulations for math and science education in grades 3–12. FreeFem++ Javascript Version – FreeFem++ is a free and open source PDE solver using the finite element method. GNU Octave web interfaces – MATLAB compatible open-source software Lanner Group Ltd L-SIM Server – Java-based discrete-event simulation engine which supports model standards such as BPMN 2.0 Nanohub – web 2.0 in-browser interactive simulation of nanotechnology NetLogo – a multi-agent programming language and integrated modeling environment that runs on the Java Virtual Machine OpenPlaG – PHP-based function graph plotter for the use on websites OpenEpi – web-based packet of tools for biostatistics Recursive Porous Agent Simulation Toolkit (Repast) – agent-based modeling and simulation toolkit implemented in Java and many other languages SageMath – open-source numerical-analysis software with web interface, based on the Python programming language SimScale – web-based simulation platform supporting computational fluid dynamics, solid mechanics, and thermodynamics StarLogo – agent-based simulation language written in Java. VisSim viewer – graphically programmed data-flow diagrams for simulation of dynamical systems webMathematica and Mathematica Player – a computer algebra system and programming language. VisualSim Architect – VisualSim Explorer enables system-level models to be embedded in documents for viewing, simulation and analysis from within a web browser without any local software installation.
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ACL Data Collection Initiative

The ACL Data Collection Initiative (ACL/DCI) was a project established in 1989 by the Association for Computational Linguistics (ACL) to create and distribute large text and speech corpora for computational linguistics research. The initiative aimed to address the growing need for substantial text databases that could support research in areas such as natural language processing, speech recognition, and computational linguistics. By 1993, the initiative’s activities had effectively ceased, with its functions and datasets absorbed by the Linguistic Data Consortium (LDC), which was founded in 1992. == Objectives == The ACL/DCI had several key objectives: To acquire a large and diverse text corpus from various sources To transform the collected texts into a common format based on the Standard Generalized Markup Language (SGML) To make the corpus available for scientific research at low cost with minimal restrictions To provide a common database that would allow researchers to replicate or extend published results To reduce duplication of effort among researchers in obtaining and preparing text data These objectives were designed to address the growing demand for very large amounts of text arising from applications in recognition and analysis of text and speech. Its core objective was to "oversee the acquisition and preparation of a large text corpus to be made available for scientific research at cost and without royalties". == History == By the late 1980s, researchers in computational linguistics and speech recognition faced a significant problem: the lack of large-scale, accessible text corpora for developing statistical models and testing algorithms. Existing generally available text databases were too small to meet the needs of developing applications in text and speech recognition. The initiative was formed to meet this need by collecting, standardizing, and distributing large quantities of text data with minimal restrictions for scientific research. As stated by Liberman (1990), "research workers have been severely hampered by the lack of appropriate materials, and specially by the lack of a large enough body of text on which published results can be replicated or extended by others." The ACL/DCI committee was established in February 1989. The committee included members from academic and industrial research laboratories in the United States and Europe. The initiative was chaired by Mark Liberman from the University of Pennsylvania (formerly of AT&T Bell Laboratories). Other committee members included representatives from organizations such as Bellcore, IBM T.J. Watson Research Center, Cambridge University, Virginia Polytechnic Institute & State University, Northeastern University, University of Pennsylvania, SRI International, MCC, Xerox PARC, ISSCO, and University of Pisa. The project operated initially without dedicated funding, relying on volunteer efforts from committee members and their affiliated institutions. Key supporters included AT&T Bell Labs, Bellcore, IBM, Xerox, and the University of Pennsylvania, which allowed the use of their computing facilities for ACL/DCI-related work. Previously running on volunteer effort pro bono, in 1991, it obtained funding from General Electric and the National Science Foundation (IRI-9113530). == Data == As of 1990, the ACL/DCI had collected hundreds of millions of words of diverse text. The collection included: Wall Street Journal articles (25 to 50 million words); Canadian Hansard (parliamentary records) in parallel English and French versions: cleaned-up English Hansard donated by the IBM alignment models group (100 million words), and original Bilingual Hansard (from a different time period) obtained directly (200 million words). Collins English Dictionary (1979 edition), both as fulltext (3 million words) and as various "database" versions, constructed using "typographers' tape" donated by Collins, which were computer tapes containing the structured digital data used to typeset and print the 1979 edition of the dictionary; Emails from ARPANET newsletters for the ACM Special Interest Group on Information Retrieval Forum (IRLIST) and AIList Digest issues distributed over the ARPANET (AILIST) (5 million words), both collected by Edward A. Fox at VIPSU; Articles on networking (2 million words); U.S. Department of Agriculture Extension Service Fact Sheets (>1 million words); 200,000 scientific abstracts of about 1,500 words each from the Department of Energy (25 million words); Archives of the Challenger Investigation Commission, including transcripts of depositions and hearings (2.5 million words); Books from the Library of America, including works by Mark Twain, Eugene O'Neill, Ralph Waldo Emerson, Herman Melville, W.E.B. DuBois, Willa Cather, and Benjamin Franklin (130 books, 20 million words); Public domain books like the King James Bible, Tristram Shandy, The Federalist Papers; Several million words of transcribed radiologists' reports, donated by Francis Ganong at Kurzweil Applied Intelligence Inc (about 5 million words); The Child Language Data Exchange corpus of child language acquisition transcripts; U.S. Department of Justice Justice Retrieval and Inquiry System (JURIS) materials; The Swiss Civil Code in parallel German, French and Italian; Economic reports from the Union Bank of Switzerland, in parallel English, German, French and Italian; About 12K words of administrative policy manuals and 14K words of administrative memos, contributed by Geoff Pullum of U.C.S.C.; Material from various ACM journals and the ACL journal Computational Linguistics; The CSLI publications series: 50-100 reports (8K words each) and 5-10 books (80K words each). The initiative started with North American English text but expanded to include Canadian French and planned to include Japanese, Chinese, and other Asian languages. At least 5 million words from the collection were tagged under the Penn Treebank project, and those tags were distributed by DCI as well. After DCI was absorbed by the LDC, the datasets were curated under LDC. == Format == The ACL/DCI corpus was coded in a standard form based on SGML (Standard Generalized Markup Language, ISO 8879), consistent with the recommendations of the Text Encoding Initiative (TEI), of which the DCI was an affiliated project. The TEI was a joint project of the ACL, the Association for Computers and the Humanities, and the Association for Literary and Linguistic Computing, aiming to provide a common interchange format for literary and linguistic data. The initiative planned to add annotations reflecting consensually approved linguistic features like part of speech and various aspects of syntactic and semantic structure over time. == Examples == As an example of the use of ACL/DCI, consider the Wall Street Journal (WSJ) corpus for speech recognition research. The WSJ corpus was used as the basis for the DARPA Spoken Language System (SLS) community's Continuous Speech Recognition (CSR) Corpus. The WSJ corpus became a standard benchmark for evaluating speech recognition systems and has been used in numerous research papers. The WSJ CSR Corpus provided DARPA with its first general-purpose English, large vocabulary, natural language, high perplexity corpus containing speech (400 hours) and text (47 million words) during 1987–89. The text corpus was 313 MB in size. The text was preprocessed to remove ambiguity in the word sequence that a reader might choose, ensuring that the unread text used to train language models was representative of the spoken test material. The preprocessing included converting numbers into orthographics, expanding abbreviations, resolving apostrophes and quotation marks, and marking punctuation. As another example, the Yarowsky algorithm used bitext data from DCI to train a simple word-sense disambiguation model that was competitive with advanced models trained on smaller datasets. == Distribution == Materials from the ACL/DCI collection were distributed to research groups on a non-commercial basis. By 1990, about 25 research groups and individual researchers had received tapes containing various portions of the collected material. To obtain the data, researchers had to sign an agreement not to redistribute the data or make direct commercial use of it. However, commercial application of "analytical materials" derived from the text, such as statistical tables or grammar rules, was explicitly permitted. The initiative first distributed data via 12-inch reels of 9-track tape, then via CD-ROMs. Each such tape could contain 30 million words compressed via the Lempel-Ziv algorithms. The first CD-ROM distribution was in 1991, funded by Dragon Systems Inc. It contained Collins English Dictionary, WSJ, scientific abstracts provided by the U.S. Department of Energy, and the Penn Treebank.
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Application framework

In computer programming, an application framework consists of a software framework used by software developers to implement the standard structure of application software. Application frameworks became popular with the rise of graphical user interfaces (GUIs), since these tended to promote a standard structure for applications. Programmers find it much simpler to create automatic GUI creation tools when using a standard framework, since this defines the underlying code structure of the application in advance. Developers usually use object-oriented programming (OOP) techniques to implement frameworks such that the unique parts of an application can simply inherit from classes extant in the framework. == Examples == Apple Computer developed one of the first commercial application frameworks, MacApp (first release 1985), for the Macintosh. Originally written in an extended (object-oriented) version of Pascal termed Object Pascal, it was later rewritten in C++. Another notable framework for the Mac is Metrowerks' PowerPlant, based on Carbon. Cocoa for macOS offers a different approach to an application framework, based on the OpenStep framework developed at NeXT. Since the 2010s, many apps have been created with the frameworks based on Google's Chromium project. The two prominent ones are Electron and the Chromium Embedded Framework. Free and open-source software frameworks exist as part of the Mozilla, LibreOffice, GNOME, KDE, NetBeans, and Eclipse projects. Microsoft markets a framework for developing Windows applications in C++ called the Microsoft Foundation Class Library, and a similar framework for developing applications with Visual Basic or C#, named .NET Framework. Several frameworks can build cross-platform applications for Linux, Macintosh, and Windows from common source code, such as Qt, wxWidgets, Juce, Fox toolkit, or Eclipse Rich Client Platform (RCP). Oracle Application Development Framework (Oracle ADF) aids in producing Java-oriented systems. Silicon Laboratories offers an embedded application framework for developing wireless applications on its series of wireless chips.
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Morphobank

MorphoBank is a web application for collaborative evolutionary research, specifically phylogenetic systematics or cladistics, on the phenotype. Historically, scientists conducting research on phylogenetic systematics have worked individually or in small groups employing traditional single-user software applications such as MacClade, Mesquite and Nexus Data Editor. As the hypotheses under study have grown more complex, large research teams have assembled to tackle the problem of discovering the Tree of Life for the estimated 4-100 million living species(Wilson 2003, pp. 77–80) and the many thousands more extinct species known from fossils. Because the phenotype is fundamentally visual, and as phenotype-based phylogenetic studies have continued to increase in size, it becomes important that observations be backed up by labeled images. Traditional desktop software applications currently in wide use do not provide robust support for team-based research or for image manipulation and storage. MorphoBank is a particularly important tool for the growing scientific field of phenomics. The development of MorphoBank, which began in 2001, has been funded by the National Science Foundation's Directorates for Geosciences, Biological Sciences and Computer and Information Science and Engineering. The significance of the scientific work on MorphoBank has been featured in the New York Times(here and here), among other publications. == Advantages == Teams of scientists studying phylogenetics to build the Tree of Life assemble large spreadsheets of observations about species (referred to as "matrices"). These teams require simultaneous access by each team member to a single and secure copy of the team's data during a scientific research project. This single copy of the data also changes with great frequency during the data collection phase. Images that can be very helpful for documenting homology statements must be displayed, labeled and shared as homology statements develop. This cannot be accomplished elegantly with a desktop software package alone because in a desktop environment each collaborator is working on his own private copy of project data. Changes made by one participant cannot automatically propagate to others, preventing collaborators from seeing each other's data edits until they are manually (and due to the effort involved, often only periodically) merged into a single "true" dataset. In all but the smallest and most disciplined of teams, file version control and the reconciliation of changes made on multiple copies of the data emerge quickly as significant drags on productivity. MorphoBank is an attempt to address these issues by leveraging the ubiquity of the web and modern web-based application techniques, including Ajax, web service layers, and rich web applications to provide a full-featured, net-accessible collaborative workspace for phylogenetic research. In particular, MorphoBank makes it easy to: Share all kinds of data with geographically separated team members, including taxonomy, character and specimen data, media (including images, video and audio), phylogenetic matrices (including data in the widely used NEXUS and TNT format) and other data such as documents and genetic sequences. Label high-resolution images using a web-based image annotation application. Collaboratively edit project data such as phylogenetic matrices using a built-in web-based matrix editor. The editor allows the linking of labeled images to individual cells of a matrix. Manage access to project data. Access ranges from full-access for team members to anonymous read-only access for potential reviewers. Publish completed project data on the web in support of a published paper with a persistent URL. Search The Encyclopedia of Life for taxon exemplar images. Store high resolution CT data Create ontologies for updating and populating matrix cells. These tasks are difficult or impossible in most existing software applications. == History == In 2001 the National Science Foundation (NSF) sponsored a workshop, at the American Museum of Natural History in New York to develop the outlines of a web-based system for a collaborative, media-rich research tool for morphological phylogenetics. An application prototype presented at the workshop was later refined with feedback from the workshop and became MorphoBank version 1.0. A grant from the US National Oceanic and Atmospheric Administration funded further revisions resulting in version 2.0, released in 2005. Current support from the NSF is funding current feature enhancements to MorphoBank. MorphoBank was hosted by Stony Brook University until late October 2021 and received back up support from the American Museum of Natural History. The current version is 3.0. Rationale for the software was described in the journal Cladistics. MorphoBank has also received support from NESCENT and the San Diego Supercomputer Center. Since 2018, MorphoBank has been supported in part by Phoenix Bioinformatics, a non-profit company founded to sustain databases for the basic sciences. A permanent move of MorphoBank from Stony Brook University to Phoenix Bioinformatics was complete in late October 2021. The San Diego Supercomputer Center has previously provided technical and hosting resources to the MorphoBank project. == Usage == MorphoBank hosts the products of peer-reviewed scientific research on phenotypes. An increasing volume of systematics data is "born digital" and MorphoBank is well suited to handle this type of material. On August 24, 2007, 62 active research projects were hosted by MorphoBank, as well as 6 completed (and published) projects. By 2017 over 2000 scientists and their students were registered content builders (users are not required to register and are even more numerous) and has more than 500 publicly available projects with approximately 80,000 images that are the products of scientific research. Over 1,500 active research projects are hosted by MorphoBank. The software has been used to assemble phylogenetic research on such groups as mammals, from bats to whales, bivalve molluscs, arachnids, fossil plants and living and extinct amniotes. It has also been used more broadly in evolutionary and paleontological research to host curated images associated with published research on lacewing insects geckos, raptor birds, dinosaurs, frogs and nematodes. MorphoBank is increasingly used in conjunction with the Paleobiology Database. Example published projects: Project 1097: Blank CE, 2013 Origin and early evolution of photosynthetic eukaryotes in freshwater environments – reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution Project 2520: Carvalho, T. P., R. E. Reis, and J. P. Friel, 2017 A new species of Hoplomyzon (Siluriformes: Aspredinidae) from Maracaibo Basin, Venezuela: osteological description using high-resolution Project 2651: Baron, M. G., Norman, D. B., Barrett, P. M., 2017 A new hypothesis of dinosaur relationships and early dinosaur evolution MorphoBank has been particularly important to the Assembling the Tree of Life initiative sponsored by the National Science Foundation. MorphoBank is well-suited to such projects because of its tools for merging taxonomic, character and matrix-based data, as well as its collaborative features. Highlights of this research include a collaborative matrix on mammal evolution published in Science that included over 4,000 phenomic characters scored for over 80 species, a matrix on extant baleen whales featuring nearly 600 images, and more.
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