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88-618: Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. These data types include mutant phenotypes ; molecular characterization of mutant alleles ; and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models, and molecular classification of gene product functions. Query tools allow navigation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from

176-549: A declaratory judgment action in the United States District Court for the Northern District of California on January 20, 2006, seeking a judicial determination that Internet Archive did not violate Shell's copyright . Shell responded and brought a countersuit against Internet Archive for archiving her site, which she alleges is in violation of her terms of service . On February 13, 2007,

264-562: A pornographic actor named Daniel Davydiuk tried to remove archived images of himself from the Wayback Machine's archive, first by sending multiple DMCA requests to the archive, and then by appealing to the Federal Court of Canada . The images were removed from the website in 2017. In 2018, archives of stalkerware application FlexiSpy's website were removed from the Wayback Machine. The company claimed to have contacted

352-484: A bird feeds a brood parasite such as a cuckoo , it is unwittingly extending its phenotype; and when genes in an orchid affect orchid bee behavior to increase pollination, or when genes in a peacock affect the copulatory decisions of peahens, again, the phenotype is being extended. Genes are, in Dawkins's view, selected by their phenotypic effects. Other biologists broadly agree that the extended phenotype concept

440-414: A calendar layout with circles whose width visualizes the number of crawls each day, but no marking of duplicates with asterisks or an advanced search page. A top toolbar was added to facilitate navigating between captures. A bar chart visualizes the frequency of captures per month over the years. Features like "Changes", "Summary", and a graphical site map were added subsequently. In March that year, it

528-550: A ceremony at the University of California, Berkeley . By the time the Wayback Machine launched, it already contained over 10 billion archived pages. The data is stored on the Internet Archive's large cluster of Linux nodes. It revisits and archives new versions of websites on occasion (see technical details below). Sites can also be captured manually by entering a website's URL into the search box, provided that

616-518: A gene has on its surroundings, including other organisms, as an extended phenotype, arguing that "An animal's behavior tends to maximize the survival of the genes 'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it." For instance, an organism such as a beaver modifies its environment by building a beaver dam ; this can be considered an expression of its genes , just as its incisor teeth are—which it uses to modify its environment. Similarly, when

704-477: A given Web page was accessible to the public. These dates are used to determine if a Web page is available as prior art for instance in examining a patent application. There are technical limitations to archiving a website, and as a consequence, opposing parties in litigation can misuse the results provided by website archives. This problem can be exacerbated by the practice of submitting screenshots of web pages in complaints, answers, or expert witness reports when

792-540: A judge for the United States District Court for the District of Colorado dismissed all counterclaims except breach of contract . The Internet Archive did not move to dismiss the copyright infringement claims that Shell asserted arose out of its copying activities, which would also go forward. On April 25, 2007, Internet Archive and Suzanne Shell jointly announced the settlement of their lawsuit. The Internet Archive said it "...has no interest in including materials in

880-529: A large part of the Human Genome Project . Phenomics has applications in agriculture. For instance, genomic variations such as drought and heat resistance can be identified through phenomics to create more durable GMOs. Phenomics may be a stepping stone towards personalized medicine , particularly drug therapy . Once the phenomic database has acquired enough data, a person's phenomic information can be used to select specific drugs tailored to

968-439: A little about. Searching can be performed within D. melanogaster only or within all species. Data other than genes can be searched using the ‘data class’ menu. The following provides two examples of research that is related to or uses FlyBase: Phenotypes In genetics , the phenotype (from Ancient Greek φαίνω ( phaínō )  'to appear, show' and τύπος ( túpos )  'mark, type')

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1056-537: A multidimensional search space with several neurobiological levels, spanning the proteome, cellular systems (e.g., signaling pathways), neural systems and cognitive and behavioural phenotypes." Plant biologists have started to explore the phenome in the study of plant physiology. In 2009, a research team demonstrated the feasibility of identifying genotype–phenotype associations using electronic health records (EHRs) linked to DNA biobanks . They called this method phenome-wide association study (PheWAS). Inspired by

1144-420: A new data centre in a Sun Modular Datacenter on Sun Microsystems ' California campus. As of 2009 , the Wayback Machine contained approximately three petabytes of data and was growing at a rate of 100 terabytes each month. A new, improved version of the Wayback Machine, with an updated interface and a fresher index of archived content, was made available for public testing in 2011, where captures appear in

1232-453: A particular enzyme is expressed at high levels, the organism may produce more of that enzyme and exhibit a particular trait as a result. On the other hand, if the gene is expressed at low levels, the organism may produce less of the enzyme and exhibit a different trait. Gene expression is regulated at various levels and thus each level can affect certain phenotypes, including transcriptional and post-transcriptional regulation. Changes in

1320-494: A predetermined number of hyperlinks based on a preset depth limit, so it cannot archive every hyperlink on every page. In a 2009 case, Netbula, LLC v. Chordiant Software Inc. , defendant Chordiant filed a motion to compel Netbula to disable the robots.txt file on its website that was causing the Wayback Machine to retroactively remove access to previous versions of pages it had archived from Netbula's site, pages that Chordiant believed would support its case. Netbula objected to

1408-501: A site blocked the Internet Archive, any previously archived pages from the domain were immediately rendered unavailable as well. In addition, the Internet Archive stated that "Sometimes, a website owner will contact us directly and ask us to stop crawling or archiving a site. We comply with these requests." In addition, the website says: "The Internet Archive is not interested in preserving or offering access to Web sites or other internet documents of persons who do not want their materials in

1496-515: A site might be included in more than one crawl list, so how often a site is crawled varies widely. A "Save Page Now" archiving feature was made available in October 2013, accessible on the lower right of the Wayback Machine's main page. Once a target URL is entered and saved, the web page will become part of the Wayback Machine. Through the Internet address web.archive.org, users can upload to

1584-414: A specific gene, protein, or region across the species. When looking for cytology there are two main tools available. Use Cytosearch when looking for cytologically-mapped genes or deficiencies, that have not been molecularly mapped to the sequence. Use Gbrowse when looking for molecularly mapped sequences, insertions, or Affymetrix probes. There are two main query tools in FlyBase. The first main query tool

1672-479: A user commented, "There needs to be a Scientists' March on Washington". The site is used heavily for verification, providing access to references and content creation by Misplaced Pages editors . When new URLs are added to Misplaced Pages, the Internet Archive has been archiving them. In September 2020, a partnership was announced with Cloudflare to automatically archive websites served via its "Always Online" service, which will also allow it to direct users to its copy of

1760-672: Is based in part upon Recommendations for Managing Removal Requests and Preserving Archival Integrity , known as The Oakland Archive Policy , published by the School of Information Management and Systems at University of California, Berkeley in 2002, which gives a website owner the right to block access to the site's archives. Wayback has complied with this policy to help avoid expensive litigation. The Wayback retroactive exclusion policy began to relax in 2017, when it stopped honoring robots on U.S. government and military web sites for both crawling and displaying web pages. As of April 2017, Wayback

1848-412: Is called Jump to Gene (J2G). This is found in the top right of the blue navigation bar on every page of FlyBase. This tool is useful when you know exactly what you are looking for and want to go to the report page with that data. The second main query tool is called QuickSearch. This is located on the FlyBase homepage. This tool is most useful when you want to look up something quickly that you may only know

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1936-659: Is carried out by a consortium of Drosophila researchers and computer scientists at Harvard University and Indiana University in the United States, and University of Cambridge in the United Kingdom. FlyBase is one of the organizations contributing to the Generic Model Organism Database (GMOD). As of 2022 the FlyBase home page requested a website access fee of US$ 150.00 per person per year, stating that "The NHGRI has reduced

2024-414: Is for complex querying, filtering, and analysis of captured data. Historically, the Wayback Machine has respected the robots exclusion standard (robots.txt) in determining if a website would be crawled – or if already crawled, if its archives would be publicly viewable. Website owners had the option to opt out of Wayback Machine through the use of robots.txt. It applied robots.txt rules retroactively; if

2112-463: Is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs , where the plants are bushy with broad leaves and expanded inflorescences ; the other is among sand dunes where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine

2200-466: Is ignoring robots.txt more broadly, not just for U.S. government websites. From its public launch in 2001, the Wayback Machine has been studied by scholars both for the ways it stores and collects data as well as for the actual pages contained in its archive. As of 2013, scholars had written about 350 articles on the Wayback Machine, mostly from the information technology , library science , and social science fields. Social science scholars have used

2288-417: Is problematic. A proposed definition for both terms as the "physical totality of all traits of an organism or of one of its subsystems" was put forth by Mahner and Kary in 1997, who argue that although scientists tend to intuitively use these and related terms in a manner that does not impede research, the terms are not well defined and usage of the terms is not consistent. Some usages of the term suggest that

2376-478: Is relevant, but consider that its role is largely explanatory, rather than assisting in the design of experimental tests. Phenotypes are determined by an interaction of genes and the environment, but the mechanism for each gene and phenotype is different. For instance, an albino phenotype may be caused by a mutation in the gene encoding tyrosinase which is a key enzyme in melanin formation. However, exposure to UV radiation can increase melanin production, hence

2464-467: Is restricted by the publisher or stored in databases that are not accessible. To overcome inconsistencies in partially cached websites, Archive-It.org was developed in 2005 by the Internet Archive as a means of allowing institutions and content creators to voluntarily harvest and preserve collections of digital content, and create digital archives. Crawls are contributed from various sources, some imported from third parties and others generated internally by

2552-412: Is the hypothesized pre-cellular stage in the evolutionary history of life on earth, in which self-replicating RNA molecules proliferated prior to the evolution of DNA and proteins. The folded three-dimensional physical structure of the first RNA molecule that possessed ribozyme activity promoting replication while avoiding destruction would have been the first phenotype, and the nucleotide sequence of

2640-479: Is the set of observable characteristics or traits of an organism . The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological properties, its behavior , and the products of behavior. An organism's phenotype results from two basic factors: the expression of an organism's genetic code (its genotype ) and the influence of environmental factors. Both factors may interact, further affecting

2728-556: Is under siege ". The Wayback Machine's software has been developed to " crawl " the Web and download all publicly accessible information and data files on webpages, the Gopher hierarchy, the Netnews (Usenet) bulletin board system, and downloadable software. The information collected by these "crawlers" does not include all the information available on the Internet, since much of the data

FlyBase - Misplaced Pages Continue

2816-550: The genotype–phenotype distinction in 1911 to make clear the difference between an organism's hereditary material and what that hereditary material produces. The distinction resembles that proposed by August Weismann (1834–1914), who distinguished between germ plasm (heredity) and somatic cells (the body). More recently, in The Selfish Gene (1976), Dawkins distinguished these concepts as replicators and vehicles. Despite its seemingly straightforward definition,

2904-554: The Archive would have to delete pages from its system upon request of the creator. The exclusion policies for the Wayback Machine may be found in the FAQ section of the site. Some cases have been brought against the Internet Archive specifically for its Wayback Machine archiving efforts. In late 2002, the Internet Archive removed various sites that were critical of Scientology from the Wayback Machine. An error message stated that this

2992-864: The Archive. For example, crawls are contributed by the Sloan Foundation and Alexa , crawls run by Internet Archive on behalf of NARA and the Internet Memory Foundation , mirrors of Common Crawl . The "Worldwide Web Crawls" have been running since 2010 and capture the global Web. In September 2020, the Internet Archive announced a partnership with Cloudflare – an American content delivery network service provider – to automatically index websites served via its "Always Online" services. Documents and resources are stored with time stamp URLs such as 20241124103401 . Pages' individual resources such as images and style sheets and scripts, as well as outgoing hyperlinks , are linked to with

3080-595: The Drosophila Information Service (DIS), which dates back to 1934 when the field was starting to spread from Thomas Hunt Morgan 's lab. Material in these pages presented regular 'catalogs' of mutations, and bibliographies of the Drosophila literature. As computer infrastructure developed in the '80s and '90s, these newsletters gave way and merged with internet mailing lists, and these eventually became online resources and data. In 1992, data on

3168-478: The FlyBase project was carried out by a consortium of Drosophila researchers and computer scientists at Harvard University , University of Cambridge (UK), Indiana University and the University of New Mexico . FlyBase contains a complete annotation of the Drosophila melanogaster genome that is updated several times per year. It also included a searchable bibliography of research on Drosophila genetics in

3256-407: The Northern District of California, San Jose Division, rejected Netbula's arguments and ordered them to disable the robots.txt blockage temporarily in order to allow Chordiant to retrieve the archived pages that they sought. In an October 2004 case, Telewizja Polska USA, Inc. v. Echostar Satellite , No. 02 C 3293, 65 Fed. R. Evid. Serv. 673 (N.D. Ill. October 15, 2004), a litigant attempted to use

3344-422: The Wayback Machine a large variety of contents, including PDF and data compression file formats. The Wayback Machine creates a permanent local URL of the upload content, that is accessible in the web, even if not listed while searching in the https://archive.org official website. Starting in October 2019, users were limited to 15 archival requests and retrievals per minute. As technology has developed over

3432-469: The Wayback Machine archives as a source of admissible evidence, perhaps for the first time. Telewizja Polska is the provider of TVP Polonia and EchoStar operates the Dish Network . Prior to the trial proceedings, EchoStar indicated that it intended to offer Wayback Machine snapshots as proof of the past content of Telewizja Polska's website. Telewizja Polska brought a motion in limine to suppress

3520-423: The Wayback Machine contained over 25 petabytes of data. As of December 2020, the Wayback Machine contained over 70 petabytes of data. The Wayback Machine service offers three public APIs, SavePageNow, Availability, and CDX. SavePageNow can be used to archive web pages. Availability API for checking the archive availability status for a web page, checking whether an archive for the web page exists or not. CDX API

3608-618: The Wayback Machine has been unable to display YouTube comments when saving videos' watch pages, as, according to the Archive Team, comments are no longer "loaded within the page itself." The Wayback Machine's web crawler has difficulty extracting anything not coded in HTML or one of its variants, which can often result in broken hyperlinks and missing images. Due to this, the web crawler cannot archive "orphan pages" that are not linked to by other pages. The Wayback Machine's crawler only follows

FlyBase - Misplaced Pages Continue

3696-433: The Wayback Machine of persons who do not wish to have their Web content archived. We recognize that Ms. Shell has a valid and enforceable copyright in her Web site and we regret that the inclusion of her Web site in the Wayback Machine resulted in this litigation." Shell said, "I respect the historical value of Internet Archive's goal. I never intended to interfere with that goal nor cause it any harm." Between 2013 and 2016,

3784-587: The Wayback Machine to analyze how the development of websites from the mid-1990s to the present has affected the company's growth. When the Wayback Machine archives a page, it usually includes most of the hyperlinks, keeping those links active when they just as easily could have been broken by the Internet's instability. Researchers in India studied the effectiveness of the Wayback Machine's ability to save hyperlinks in online scholarly publications and found that it saved slightly more than half of them. "Journalists use

3872-456: The Wayback Machine to view dead websites, dated news reports, and changes to website contents. Its content has been used to hold politicians accountable and expose battlefield lies." In 2014, an archived social media page of Igor Girkin , a separatist rebel leader in Ukraine, showed him boasting about his troops having shot down a suspected Ukrainian military airplane before it became known that

3960-458: The Wayback Machine's storage capacity by 700 terabytes. In January 2013, the company announced a milestone of 240 billion URLs. In October 2013, the company introduced the "Save a Page" feature, which allows any Internet user to archive the contents of a URL, and quickly generates a permanent link unlike the preceding liveweb feature. In December 2014, the Wayback Machine contained 435 billion web pages—almost nine petabytes of data, and

4048-419: The archive calls a "three-dimensional index". Kahle and Gilliat created the machine hoping to archive the entire Internet and provide "universal access to all knowledge". The name "Wayback Machine" is a reference to a fictional time-traveling device in the animated cartoon The Adventures of Rocky and Bullwinkle and Friends from the 1960s. In a segment of the cartoon entitled "Peabody's Improbable History",

4136-412: The characters Mister Peabody and Sherman use the " Wayback Machine " to travel back in time to witness and participate in famous historical events. From 1996 to 2001, the information was kept on digital tape, with Kahle occasionally allowing researchers and scientists to tap into the "clunky" database . When the archive reached its fifth anniversary in 2001, it was unveiled and opened to the public in

4224-440: The collection." On April 17, 2017, reports surfaced of sites that had gone defunct and became parked domains that were using robots.txt to exclude themselves from search engines, resulting in them being inadvertently excluded from the Wayback Machine. Following this, the Internet Archive changed the policy to require an explicit exclusion request to remove sites from the Wayback Machine. Wayback's retroactive exclusion policy

4312-450: The concept of the phenotype has hidden subtleties. It may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins . Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by Western blotting ) and are thus part of the phenotype; human blood groups are an example. It may seem that this goes beyond

4400-517: The context of phenotype prediction. Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word phenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as phenomics . Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness. Phenomics forms

4488-483: The corresponding amino acid sequence of a gene may change the frequency of guanine - cytosine base pairs ( GC content ). These base pairs have a higher thermal stability ( melting point ) than adenine - thymine , a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content. Richard Dawkins described a phenotype that included all effects that

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4576-631: The data. In October 1992, the National Center for Human Genome Research of the NIH funded the FlyBase project with the objective of designing, building and releasing a database of genetic and molecular information concerning Drosophila melanogaster . FlyBase also receives support from the Medical Research Council , London. In 1998, the FlyBase consortium integrated the information into a single Drosophila genomics server. As of 2022

4664-501: The database are the large multispecies data sets deposited by the Drosophila 12 Genomes Consortium (Clark et al 2007) and Crosby et al 2007. Search Strategies—Gene reports for genes from all twelve sequenced Drosophila genomes are available in FlyBase. There are four main ways this data can be browsed: Precomputed Files BLAST, Gbrowse, and Gene Report Pages. Gbrowse and precomputed files are for genome-wide analysis, bioinformatics, and comparative genomics. BLAST and gene report pages are for

4752-499: The earliest known pages was archived on May 10, 1996, at 2:08   p.m. ( UTC ). Internet Archive founders Brewster Kahle and Bruce Gilliat launched the Wayback Machine in San Francisco , California , in October 2001, primarily to address the problem of web content vanishing whenever it gets changed or when a website is shut down. The service enables users to see archived versions of web pages across time, which

4840-415: The environment plays a role in this phenotype as well. For most complex phenotypes the precise genetic mechanism remains unknown. For instance, it is largely unclear how genes determine the shape of bones or the human ear. Gene expression plays a crucial role in determining the phenotypes of organisms. The level of gene expression can affect the phenotype of an organism. For example, if a gene that codes for

4928-439: The evolution from genotype to genome to pan-genome , a concept of exploring the relationship ultimately among pan-phenome, pan-genome , and pan- envirome was proposed in 2023. Phenotypic variation (due to underlying heritable genetic variation ) is a fundamental prerequisite for evolution by natural selection . It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects

5016-440: The false statement that a "mutation has no phenotype". Behaviors and their consequences are also phenotypes, since behaviors are observable characteristics. Behavioral phenotypes include cognitive, personality, and behavioral patterns. Some behavioral phenotypes may characterize psychiatric disorders or syndromes. A phenome is the set of all traits expressed by a cell , tissue , organ , organism , or species . The term

5104-538: The first self-replicating RNA molecule would have been the original genotype. Wayback Machine The Wayback Machine is a digital archive of the World Wide Web founded by the Internet Archive , an American nonprofit organization based in San Francisco , California . Created in 1996 and launched to the public in 2001, it allows users to go "back in time" to see how websites looked in

5192-407: The funding of FlyBase by 50%". Drosophila melanogaster has been an experimental organism since the early 1900s, and has since been placed at the forefront of many areas of research. As this field of research spread and became global, researchers working on the same problems needed a way to communicate and monitor progress in the field. This niche was initially filled by community newsletters such as

5280-541: The genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection. The interaction between genotype and phenotype has often been conceptualized by the following relationship: A more nuanced version of the relationship is: Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions. The plant Hieracium umbellatum

5368-435: The genetics and genomics of D. melanogaster and related species were electronically available over the Internet through the funded FlyBase, BDGP (Berkeley Drosophila Genome Project) and EDGP (European Drosophila Genome Project) informatics groups. These groups recognized that most genome project and community data types overlapped. They decided it would be of value to present the scientific community with an integrated view of

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5456-721: The individual. Large-scale genetic screens can identify the genes or mutations that affect the phenotype of an organism. Analyzing the phenotypes of mutant genes can also aid in determining gene function. Most genetic screens have used microorganisms, in which genes can be easily deleted. For instance, nearly all genes have been deleted in E. coli and many other bacteria , but also in several eukaryotic model organisms such as baker's yeast and fission yeast . Among other discoveries, such studies have revealed lists of essential genes . More recently, large-scale phenotypic screens have also been used in animals, e.g. to study lesser understood phenotypes such as behavior . In one screen,

5544-525: The initial lawsuit was filed, the Archive should have removed all previous copies of the plaintiff website from the Wayback Machine, however, some material continued to be publicly visible on Wayback. The lawsuit was settled out of court after Wayback fixed the problem. Activist Suzanne Shell filed suit in December 2005, demanding Internet Archive pay her US$ 100,000 for archiving her website profane-justice.org between 1999 and 2004. Internet Archive filed

5632-475: The last century. Information on current researchers, and a partial pedigree of relationships between current researchers, was searchable, based on registration of the participating scientist. The site also provides a large database of images illustrating the full genome, and several movies detailing embryogenesis ( ImageBrowser Archived 2007-03-24 at the Wayback Machine ). The two major tributaries to

5720-626: The levels of gene expression can be influenced by a variety of factors, such as environmental conditions, genetic variations, and epigenetic modifications. These modifications can be influenced by environmental factors such as diet, stress, and exposure to toxins, and can have a significant impact on an individual's phenotype. Some phenotypes may be the result of changes in gene expression due to these factors, rather than changes in genotype. An experiment involving machine learning methods utilizing gene expressions measured from RNA sequencing found that they can contain enough signal to separate individuals in

5808-430: The motion on the ground that defendants were asking to alter Netbula's website and that they should have subpoenaed Internet Archive for the pages directly. An employee of Internet Archive filed a sworn statement supporting Chordiant's motion, however, stating that it could not produce the web pages by any other means "without considerable burden, expense and disruption to its operations." Magistrate Judge Howard Lloyd in

5896-619: The number of putative mutants (see table for details). Putative mutants are then tested for heritability in order to help determine the inheritance pattern as well as map out the mutations. Once they have been mapped out, cloned, and identified, it can be determined whether a mutation represents a new gene or not. These experiments showed that mutations in the rhodopsin gene affected vision and can even cause retinal degeneration in mice. The same amino acid change causes human familial blindness , showing how phenotyping in animals can inform medical diagnostics and possibly therapy. The RNA world

5984-411: The original intentions of the concept with its focus on the (living) organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits that can be made visible by some technical procedure. The term "phenotype" has sometimes been incorrectly used as a shorthand for the phenotypic difference between a mutant and its wild type , which would lead to

6072-503: The past. Its founders, Brewster Kahle and Bruce Gilliat , developed the Wayback Machine to provide "universal access to all knowledge" by preserving archived copies of defunct web pages. Launched on May 10, 1996, the Wayback Machine had saved more than 38.2 billion web pages by the end of 2009. As of November 2024, the Wayback Machine has archived more than 916 billion web pages and well over 100 petabytes of data. The Internet Archive began archiving cached web pages in 1996. One of

6160-438: The phenome of a given organism is best understood as a kind of matrix of data representing physical manifestation of phenotype. For example, discussions led by A. Varki among those who had used the term up to 2003 suggested the following definition: "The body of information describing an organism's phenotypes, under the influences of genetic and environmental factors". Another team of researchers characterize "the human phenome [as]

6248-474: The phenotype that grows. An example of random variation in Drosophila flies is the number of ommatidia , which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments. The concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, silent mutations that do not change

6336-590: The phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic . A well-documented example of polymorphism is Labrador Retriever coloring ; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddisfly larva cases and beaver dams as "extended phenotypes". Wilhelm Johannsen proposed

6424-543: The plaintiff were invalid, based on the content of their website from several years prior. The plaintiff, Healthcare Advocates, then amended their complaint to include the Internet Archive, accusing the organization of copyright infringement as well as violations of the DMCA and the Computer Fraud and Abuse Act . Healthcare Advocates claimed that, since they had installed a robots.txt file on their website, even if after

6512-523: The plane actually was a civilian Malaysian Airlines jet ( Malaysia Airlines Flight 17 ), after which he deleted the post and blamed Ukraine's military for downing the plane. In 2017, the March for Science originated from a discussion on Reddit that indicated someone had visited Archive.org and discovered that all references to climate change had been deleted from the White House website. In response,

6600-428: The role of mutations in mice were studied in areas such as learning and memory , circadian rhythmicity , vision, responses to stress and response to psychostimulants . This experiment involved the progeny of mice treated with ENU , or N-ethyl-N-nitrosourea, which is a potent mutagen that causes point mutations . The mice were phenotypically screened for alterations in the different behavioral domains in order to find

6688-509: The several ontologies used to capture functional, phenotypic, and anatomical data. The database offers several different query tools in order to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Links between FlyBase and external databases, such as BDGP or modENCODE, provide opportunities for further exploration into other model organism databases and other resources of biological and molecular information. The FlyBase project

6776-410: The site if it cannot reach the original host. In 2014, there was a six-month lag time between when a website was crawled and when it became available for viewing in the Wayback Machine. As of 2024, the lag time is 3 to 10 hours. The Wayback Machine offers only limited search facilities. Its "Site Search" feature allows users to find a site based on words describing the site, rather than words found on

6864-411: The snapshots on the grounds of hearsay and unauthenticated source, but Magistrate Judge Arlander Keys rejected Telewizja Polska's assertion of hearsay and denied TVP's motion in limine to exclude the evidence at trial. At the trial, however, District Court Judge Ronald Guzman, the trial judge, overruled Magistrate Keys' findings, and held that neither the affidavit of the Internet Archive employee nor

6952-545: The time stamp of the currently viewed page, so they are redirected automatically to their individual captures that are the closest in time. The frequency of snapshot captures varies per website. Websites in the "Worldwide Web Crawls" are included in a "crawl list", with the site archived once per crawl. A crawl can take months or even years to complete, depending on size. For example, "Wide Crawl Number 13" started on January 9, 2015, and completed on July 11, 2016. However, there may be multiple crawls ongoing at any one time, and

7040-415: The underlying links are not exposed and therefore, can contain errors. For example, archives such as the Wayback Machine do not fill out forms and therefore, do not include the contents of non- RESTful e-commerce databases in their archives. In Europe, the Wayback Machine could be interpreted as violating copyright laws. Only the content creator can decide where their content is published or duplicated so

7128-565: The underlying pages (i.e., the Telewizja Polska website) were admissible as evidence. Judge Guzman reasoned that the employee's affidavit contained both hearsay and inconclusive supporting statements, and the purported web page, printouts were not self-authenticating. The United States Patent and Trademark Office and the European Patent Office will accept date stamps from the Internet Archive as evidence of when

7216-492: The web pages themselves. The Wayback Machine does not include every web page ever made due to the limitations of its web crawler. The Wayback Machine cannot completely archive web pages that contain interactive features such as Flash platforms and forms written in JavaScript and progressive web applications , because those functions require interaction with the host website. This means that, since approximately July 9, 2013,

7304-404: The website allows the Wayback Machine to " crawl " it and save the data. On October 30, 2020, the Wayback Machine began fact-checking content. As of January 2022, domains of ad servers are disabled from capturing. In May 2021, for Internet Archive's 25th anniversary, the Wayback Machine introduced the "Wayforward Machine" which allows users to "travel to the Internet in 2046, where knowledge

7392-572: The years, the storage capacity of the Wayback Machine has grown. In 2003, after only two years of public access, the Wayback Machine was growing at a rate of 12 terabytes per month. The data is stored on PetaBox rack systems custom designed by Internet Archive staff. The first 100TB rack became fully operational in June 2004, although it soon became clear that they would need much more storage than that. The Internet Archive migrated its customized storage architecture to Sun Open Storage in 2009, and hosts

7480-405: Was first used by Davis in 1949, "We here propose the name phenome for the sum total of extragenic, non-autoreproductive portions of the cell, whether cytoplasmic or nuclear. The phenome would be the material basis of the phenotype, just as the genome is the material basis of the genotype ." Although phenome has been in use for many years, the distinction between the use of phenome and phenotype

7568-470: Was growing at about 20 terabytes a week. In July 2016, the Wayback Machine reportedly contained around 15 petabytes of data. In October 2016, it was announced that the way web pages are counted would be changed, resulting in the decrease of the archived pages counts shown. Embedded objects such as pictures, videos, style sheets, JavaScripts are no longer counted as a "web page", whereas HTML, PDF, and plain text documents remain counted. In September 2018,

7656-451: Was in response to a "request by the site owner". Later, it was clarified that lawyers from the Church of Scientology had demanded the removal and that the site owners did not want their material removed. In 2003, Harding Earley Follmer & Frailey defended a client from a trademark dispute using the Archive's Wayback Machine. The attorneys were able to demonstrate that the claims made by

7744-516: Was said on the Wayback Machine forum that "the Beta of the new Wayback Machine has a more complete and up-to-date index of all crawled materials into 2010, and will continue to be updated regularly. The index driving the classic Wayback Machine only has a little bit of material past 2008, and no further index updates are planned, as it will be phased out this year." Also in 2011, the Internet Archive installed their sixth pair of PetaBox racks which increased

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