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PubRef
PubRef.org was a short lived project that is now discontinued. The website is not accessible anymore. An old version can be accessed from the Internet Archive. They used the same name PubRef which was a service provided by PubMed for linking bibliographies, defeated by the independent service Crossref. PubRef was a composition and project management application used by researchers and students for scholarly writing and communication. PubRef uses an extended form of Markdown as a primary authoring format and converts this to JATS, the archive format used by the US National Library of Medicine. Research asset containerization Researchers manage scholarly writing projects within version-controlled file repositories called ''containers'' that function similarly to git repositories and docker containers to provide enhanced reproducibility, transparency and re-usability in digital science publishing. Manuscript writing A PubRef manuscript is a Markdown file within a ''contai ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Article Tag Suite
The Journal Article Tag Suite (JATS) is an XML format used to describe scientific literature published online. It is a technical standard developed by the National Information Standards Organization (NISO) and approved by the American National Standards Institute with the code Z39.96-2012. The NISO project was a continuation of the work done by NLM/NCBI, and popularized by the NLM's PubMed Central as a ''de facto'' standard for archiving and interchange of scientific open-access journals and its contents with XML. With the NISO standardization the NLM initiative has gained a wider reach, and several other repositories, such as SciELO and Redalyc, adopted the XML formatting for scientific articles. The JATS provides a set of XML elements and attributes for describing the textual and graphical content of journal articles as well as some non-article material such as letters, editorials, and book and product reviews. JATS allows for descriptions of the full article content or ju ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Internet Archive
The Internet Archive is an American digital library with the stated mission of "universal access to all knowledge". It provides free public access to collections of digitized materials, including websites, software applications/games, music, movies/videos, moving images, and millions of books. In addition to its archiving function, the Archive is an activist organization, advocating a free and open Internet. , the Internet Archive holds over 35 million books and texts, 8.5 million movies, videos and TV shows, 894 thousand software programs, 14 million audio files, 4.4 million images, 2.4 million TV clips, 241 thousand concerts, and over 734 billion web pages in the Wayback Machine. The Internet Archive allows the public to upload and download digital material to its data cluster, but the bulk of its data is collected automatically by its web crawlers, which work to preserve as much of the public web as possible. Its web archiving, web archive, the Wayback Machine, contains hu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reproducibility
Reproducibility, also known as replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or in a statistical analysis of a data set should be achieved again with a high degree of reliability when the study is replicated. There are different kinds of replication but typically replication studies involve different researchers using the same methodology. Only after one or several such successful replications should a result be recognized as scientific knowledge. With a narrower scope, ''reproducibility'' has been introduced in computational sciences: Any results should be documented by making all data and code available in such a way that the computations can be executed again with identical results. In recent decades, there has been a rising concern that many published scientific results fail the test of reproducibility, evoking a r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-access Archives
Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre open access, barriers to copying or reuse are also reduced or removed by applying an open license for copyright. The main focus of the open access movement is "peer reviewed research literature". Historically, this has centered mainly on print-based academic journals. Whereas non-open access journals cover publishing costs through access tolls such as subscriptions, site licenses or pay-per-view charges, open-access journals are characterised by funding models which do not require the reader to pay to read the journal's contents, relying instead on author fees or on public funding, subsidies and sponsorships. Open access can be applied to all forms of published research output, including peer-reviewed and non peer-reviewed academic journal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
YAML
YAML ( and ) (''see '') is a human-readable data-serialization language. It is commonly used for configuration files and in applications where data is being stored or transmitted. YAML targets many of the same communications applications as Extensible Markup Language (XML) but has a minimal syntax which intentionally differs from Standard Generalized Markup Language (SGML). It uses both Python-style indentation to indicate nesting, and a more compact format that uses for lists and for maps thus JSON files are valid YAML 1.2. Custom data types are allowed, but YAML natively encodes scalars (such as strings, integers, and floats), lists, and associative arrays (also known as maps, dictionaries or hashes). These data types are based on the Perl programming language, though all commonly used high-level programming languages share very similar concepts. The colon-centered syntax, used for expressing key-value pairs, is inspired by electronic mail headers as defined in , and the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reusability
In computer science and software engineering, reusability is the use of existing ''assets'' in some form within the software product development process; these ''assets'' are products and by-products of the software development life cycle and include code, software components, test suites, designs and documentation. The opposite concept of ''reusability'' is leverage, which modifies existing assets as needed to meet specific system requirements. Because reuse implies the creation of a , it is preferred over leverage. Subroutines or functions are the simplest form of reuse. A chunk of code is regularly organized using modules or namespaces into layers. Proponents claim that objects and software components offer a more advanced form of reusability, although it has been tough to objectively measure and define levels or scores of reusability. The ability to reuse relies in an essential way on the ability to build larger things from smaller parts, and being able to identify commonali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transparency (behavior)
As an ethic that spans science, engineering, business, and the humanities, transparency is operating in such a way that it is easy for others to see what actions are performed. Transparency implies openness, communication, and accountability. Transparency is practiced in companies, organizations, administrations, and communities. For example, in a business relation, fees are clarified at the outset by a transparent agent, so there are no surprises later. This is opposed to keeping this information hidden which is "non-transparent". A practical example of transparency is also when a cashier makes changes after a point of sale; they offer a transaction record of the items purchased (e.g., a receipt) as well as counting out the customer's change. In information security, transparency means keeping the arcane, underlying mechanisms hidden so as not to obstruct intended function—an almost opposite sense. It principally refers to security mechanisms that are intentionally undetectable ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Docker (software)
Docker is a set of platform as a service (PaaS) products that use OS-level virtualization to deliver software in packages called ''containers''. The service has both free and premium tiers. The software that hosts the containers is called Docker Engine. It was first started in 2013 and is developed by Docker, Inc. Background Containers are isolated from one another and bundle their own software, libraries and configuration files; they can communicate with each other through well-defined channels. Because all of the containers share the services of a single operating system kernel, they use fewer resources than virtual machines. Operation Docker can package an application and its dependencies in a virtual container that can run on any Linux, Windows, or macOS computer. This enables the application to run in a variety of locations, such as on-premises, in public (see decentralized computing, distributed computing, and cloud computing) or private cloud. When running on Linux, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PubMed
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the database as part of the Entrez system of information retrieval. From 1971 to 1997, online access to the MEDLINE database had been primarily through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997. Content In addition to MEDLINE, PubMed provides access to: * older references from the print version of ''Index Medicus'', back to 1951 and earlier * references to some journals before they were indexed in Index Medicus and MEDLINE, for instance ''Science'', ''BMJ'', and ''Annals of Surgery'' * very recent entries to records for an article before it ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Repository (version Control)
In version control systems, a repository is a data structure that stores metadata for a set of files or directory structure. Depending on whether the version control system in use is distributed, like Git or Mercurial, or centralized, like Subversion, CVS, or Perforce, the whole set of information in the repository may be duplicated on every user's system or may be maintained on a single server. Some of the metadata that a repository contains includes, among other things, a historical record of changes in the repository, a set of commit objects, and a set of references to commit objects, called ''heads''. The main purpose of a repository is to store a set of files, as well as the history of changes made to those files. Exactly how each version control system handles storing those changes, however, differs greatly. For instance, Subversion in the past relied on a database instance but has since moved to storing its changes directly on the filesystem. These differences in storage te ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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