A cellular evolutionary algorithm (cEA) is a kind of evolutionary algorithm (EA) in which individuals cannot mate arbitrarily, but every one interacts with its closer neighbors on which a basic EA is applied (selection, variation, replacement). The cellular model simulates natural evolution from the point of view of the individual, which encodes a tentative optimization, learning, or search problem solution. The essential idea of this model is to provide the EA population with a special structure defined as a connected graph, in which each vertex is an individual who communicates with his nearest neighbors. Particularly, individuals are conceptually set in a toroidal mesh, and are only allowed to recombine with close individuals. This leads to a kind of locality known as "isolation by distance". The set of potential mates of an individual is called its "neighborhood". It is known that, in this kind of algorithm, similar individuals tend to cluster creating niches, and these groups operate as if they were separate sub-populations (islands). There is no clear borderline between adjacent groups, and close niches could be easily colonized by competitive niches and potentially merge solution contents during the process. Simultaneously, farther niches can be affected more slowly. == Introduction == A cellular evolutionary algorithm (cEA) usually evolves a structured bidimensional grid of individuals, although other topologies are also possible. In this grid, clusters of similar individuals are naturally created during evolution, promoting exploration in their boundaries, while exploitation is mainly performed by direct competition and merging inside them. The grid is usually 2D toroidal structure, although the number of dimensions can be easily extended (to 3D) or reduced (to 1D, e.g. a ring). The neighborhood of a particular point of the grid (where an individual is placed) is defined in terms of the Manhattan distance from it to others in the population. Each point of the grid has a neighborhood that overlaps the neighborhoods of nearby individuals. In the basic algorithm, all the neighborhoods have the same size and identical shapes. The two most commonly used neighborhoods are L5, also called the Von Neumann or NEWS (North, East, West and South) neighborhood, and C9, also known as the Moore neighborhood. Here, L stands for "linear" while C stands for "compact". In cEAs, the individuals can only interact with their neighbors in the reproductive cycle where the variation operators are applied. This reproductive cycle is executed inside the neighborhood of each individual and, generally, consists in selecting two parents among its neighbors according to a certain criterion, applying the variation operators to them (recombination and mutation for example), and replacing the considered individual by the recently created offspring following a given criterion, for instance, replace if the offspring represents a better solution than the considered individual. == Synchronous versus asynchronous == In a regular synchronous cEA, the algorithm proceeds from the very first top left individual to the right and then to the several rows by using the information in the population to create a new temporary population. After finishing with the bottom-right last individual the temporary population is full with the newly computed individuals, and the replacement step starts. In it, the old population is completely and synchronously replaced with the newly computed one according to some criterion. Usually, the replacement keeps the best individual in the same position of both populations, that is, elitism is used. According to the update policy of the population used, an asynchronous cEA may also be defined and is a well-known issue in cellular automata. In asynchronous cEAs the order in which the individuals in the grid are update changes depending on the choice of criterion: line sweep, fixed random sweep, new random sweep, and uniform choice. All four proceed using the newly computed individual (or the original if better) for the computations of its neighbors. The overlap of the neighborhoods provides an implicit mechanism of solution migration to the cEA. Since the best solutions spread smoothly through the whole population, genetic diversity in the population is preserved longer than in non structured EAs. This soft dispersion of the best solutions through the population is one of the main issues of the good tradeoff between exploration and exploitation that cEAs perform during the search. This tradeoff can be tuned (and by extension the genetic diversity level along the evolution) by modifying (for instance) the size of the neighborhood used, as the overlap degree between the neighborhoods grows according to the size of the neighborhood. A cEA can be seen as a cellular automaton (CA) with probabilistic rewritable rules, where the alphabet of the CA is equivalent to the potential number of solutions of the problem. Hence, knowledge from research in CAs can be applied to cEAs. == Parallelism == Cellular EAs are very amenable to parallelism, thus usually found in the literature of parallel metaheuristics. In particular, fine grain parallelism can be used to assign independent threads of execution to every individual, thus allowing the whole cEA to run on a concurrent or actually parallel hardware platform. In this way, large time reductions can be obtained when running cEAs on FPGAs or GPUs. However, it is important to stress that cEAs are a model of search, in many senses different from traditional EAs. Also, they can be run in sequential and parallel platforms, reinforcing the fact that the model and the implementation are two different concepts. See here for a complete description on the fundamentals for the understanding, design, and application of cEAs.
Data event
A data event is a relevant state transition defined in an event schema. Typically, event schemata are described by pre- and post condition for a single or a set of data items. In contrast to ECA (Event condition action), which considers an event to be a signal, the data event not only refers to the change (signal), but describes specific state transitions, which are referred to in ECA as conditions. Considering data events as relevant data item state transitions allows defining complex event-reaction schemata for a database. Defining data event schemata for relational databases is limited to attribute and instance events. Object-oriented databases also support collection properties, which allows defining changes in collections as data events, too.
IgHome
igHome is a customizable start page introduced in 2012 as an alternative to iGoogle, the personal web portal launched by Google in May 2005. Just like iGoogle, igHome offers users the possibility to build a start page containing a central search box and a number of gadgets. igHome mimics the user interface of iGoogle. Registered igHome users can create multiple tabs and import RSS feeds.
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.
Flektor
Flektor was a web application that allowed users the ability to create and "mashup" their own content (photos, videos, music, etc.) and share it via email, on social networking websites MySpace, Facebook, Blogger, Digg, eBay or on personal blogs. The company's website (Flektor.com) launched on April 2, 2007, and over 40,000 people began utilizing its features just one month later. Flektor closed down in January 2009. Flektor offered tools and widgets that included audio, video, photos, text, and approximately 100 effects, transitions and filters to be used with media. Users could create personalized slideshows, polls, postcards, and streaming video projects which the website calls "fleks". Flektor also offered Chat (used as a MySpace addon) and Movie Editor, which provided the ability to edit content and assets together. Users of Flektor could import media from websites like Photobucket and Google's YouTube, and then edit their content with the site's editing tools. Flektor's erstwhile competitors include Slide.com (founded by PayPal co-founder Max Levchin), RockYou!, Yahoo's JumpCut and Brightcove. == History == Flektor was created by Jason Rubin, Andy Gavin and former HBO executive Jason R. Kay. Both Rubin and Gavin spent most of their careers in the video game industry developing games for publishers like Electronic Arts, Universal Interactive Studios and Sony Computer Entertainment America. They founded a successful game development studio called Naughty Dog and were responsible for games such as Crash Bandicoot and Jak and Daxter. After selling Naughty Dog to Sony, Rubin focused on a comic book series called Iron and the Maiden before teaming up again with Gavin to venture into the web industry with Flektor. Jason Kay spent four years at Home Box Office, working as a consultant to the EVP of Business Development. They recruited former employee and then Naughty Dog Lead Programmer Scott Shumaker to lead the technology team along with Gavin. Ryan Evans joined shortly thereafter, spearheading product development. Flektor is based in Culver City, California. In May 2007, the company was sold to Fox Interactive Media, which is a division of News Corp., for more than $20 million. The deal coincided with Fox's acquisition of Photobucket, an image-hosting and sharing website. Fox Interactive Media already holds possession of MySpace, IGN Entertainment, FOXSports.com, AmericanIdol.com and Rotten Tomatoes. After the acquisition, Rubin, Gavin and Kay departed, leaving the studio in the hands of Shumaker and Evans. In the fall of 2007, Flektor partnered with its sister company, MySpace, and MTV to provide instant audience feedback via polls for the interactive MySpace/ MTV Presidential Dialogues series with presidential candidates Senator Barack Obama, Senator John McCain and John Edwards. Use of Flektor's polling system, enabled hosts John McLaughlin and Geoffrey Garin to cater their questions towards subjects of voter-interest. In the fall of 2008, Flektor built the official site for the 2008 Presidential debates, hosted at MyDebates. In January 2009, due to a company directive to focus on the core MySpace property, Fox Interactive announced that Flektor would be shut down, with some of its technology being incorporated into MySpace.
Neighborhood operation
In computer vision and image processing a neighborhood operation is a commonly used class of computations on image data which implies that it is processed according to the following pseudo code: Visit each point p in the image data and do { N = a neighborhood or region of the image data around the point p result(p) = f(N) } This general procedure can be applied to image data of arbitrary dimensionality. Also, the image data on which the operation is applied does not have to be defined in terms of intensity or color, it can be any type of information which is organized as a function of spatial (and possibly temporal) variables in p. The result of applying a neighborhood operation on an image is again something which can be interpreted as an image, it has the same dimension as the original data. The value at each image point, however, does not have to be directly related to intensity or color. Instead it is an element in the range of the function f, which can be of arbitrary type. Normally the neighborhood N is of fixed size and is a square (or a cube, depending on the dimensionality of the image data) centered on the point p. Also the function f is fixed, but may in some cases have parameters which can vary with p, see below. In the simplest case, the neighborhood N may be only a single point. This type of operation is often referred to as a point-wise operation. == Examples == The most common examples of a neighborhood operation use a fixed function f which in addition is linear, that is, the computation consists of a linear shift invariant operation. In this case, the neighborhood operation corresponds to the convolution operation. A typical example is convolution with a low-pass filter, where the result can be interpreted in terms of local averages of the image data around each image point. Other examples are computation of local derivatives of the image data. It is also rather common to use a fixed but non-linear function f. This includes median filtering, and computation of local variances. The Nagao-Matsuyama filter is an example of a complex local neighbourhood operation that uses variance as an indicator of the uniformity within a pixel group. The result is similar to a convolution with a low-pass filter with the added effect of preserving sharp edges. There is also a class of neighborhood operations in which the function f has additional parameters which can vary with p: Visit each point p in the image data and do { N = a neighborhood or region of the image data around the point p result(p) = f(N, parameters(p)) } This implies that the result is not shift invariant. Examples are adaptive Wiener filters. == Implementation aspects == The pseudo code given above suggests that a neighborhood operation is implemented in terms of an outer loop over all image points. However, since the results are independent, the image points can be visited in arbitrary order, or can even be processed in parallel. Furthermore, in the case of linear shift-invariant operations, the computation of f at each point implies a summation of products between the image data and the filter coefficients. The implementation of this neighborhood operation can then be made by having the summation loop outside the loop over all image points. An important issue related to neighborhood operation is how to deal with the fact that the neighborhood N becomes more or less undefined for points p close to the edge or border of the image data. Several strategies have been proposed: Compute result only for points p for which the corresponding neighborhood is well-defined. This implies that the output image will be somewhat smaller than the input image. Zero padding: Extend the input image sufficiently by adding extra points outside the original image which are set to zero. The loops over the image points described above visit only the original image points. Border extension: Extend the input image sufficiently by adding extra points outside the original image which are set to the image value at the closest image point. The loops over the image points described above visit only the original image points. Mirror extension: Extend the image sufficiently much by mirroring the image at the image boundaries. This method is less sensitive to local variations at the image boundary than border extension. Wrapping: The image is tiled, so that going off one edge wraps around to the opposite side of the image. This method assumes that the image is largely homogeneous, for example a stochastic image texture without large textons.
Service-oriented software engineering
Service-oriented software engineering (SOSE), also referred to as service engineering, is a software engineering methodology focused on the development of software systems by composition of reusable services (service-orientation) often provided by other service providers. Since it involves composition, it shares many characteristics of component-based software engineering, the composition of software systems from reusable components, but it adds the ability to dynamically locate necessary services at run-time. These services may be provided by others as web services, but the essential element is the dynamic nature of the connection between the service users and the service providers. == Service-oriented interaction pattern == There are three types of actors in a service-oriented interaction: service providers, service users and service registries. They participate in a dynamic collaboration which can vary from time to time. Service providers are software services that publish their capabilities and availability with service registries. Service users are software systems (which may be services themselves) that accomplish some task through the use of services provided by service providers. Service users use service registries to discover and locate the service providers they can use. This discovery and location occurs dynamically when the service user requests them from a service registry.