1.
Streptavidin
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Streptavidin /ˌstrɛpˈtævɪdɪn/ is a 52.8 kDa protein purified from the bacterium Streptomyces avidinii. Streptavidin homo-tetramers have a high affinity for biotin. With a dissociation constant on the order of ≈10−14 mol/L, the binding of biotin to streptavidin is one of the strongest non-covalent interactions known in nature, the crystal structure of streptavidin with biotin bound was reported by two groups in 1989. The structure was solved using multi wavelength anomalous diffraction by Hendrickson et al. at Columbia University, duPont Central Research and Development Department. As of September 2016, there are 167 structures deposited in the Protein Data Bank, see this link for a complete list. The secondary structure of a monomer is composed of eight antiparallel β-strands. A biotin binding-site is located at one end of each β-barrel, four identical streptavidin monomers associate to give streptavidin’s tetrameric quaternary structure. The biotin binding-site in each barrel consists of residues from the interior of the barrel, in this way, each subunit contributes to the binding site on the neighboring subunit, and so the tetramer can also be considered a dimer of functional dimers. The numerous crystal structures of the complex have shed light on the origins of the remarkable affinity. Firstly, there is high shape complementarity between the pocket and biotin. Secondly, there is a network of hydrogen bonds formed to biotin when in the binding site. There are eight hydrogen bonds directly made to residues in the site, involving residues Asn23, Tyr43, Ser27, Ser45, Asn49, Ser88, Thr90. There is also a shell of hydrogen bonding involving residues that interact with the first shell residues. However, the streptavidin-biotin affinity exceeds that which would be predicted from the bonding interactions alone. In particular, the pocket is lined with conserved tryptophan residues, most attempts at mutating streptavidin result in a lowered biotin-binding affinity, which is to be expected in such a highly optimised system. However, a recently engineered mutant of streptavidin, named traptavidin, was found to have more than ten-fold slower biotin dissociation and this decreased dissociation rate was accompanied by a two-fold decrease in the association rate. Among the most common uses are the purification or detection of various biomolecules, the strong streptavidin-biotin bond can be used to attach various biomolecules to one another or onto a solid support. Harsh conditions are needed to break the interaction, which often denatures the protein of interest being purified
2.
Software developer
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A software developer is a person concerned with facets of the software development process, including the research, design, programming, and testing of computer software. Other job titles which are used with similar meanings are programmer, software analyst. According to developer Eric Sink, the differences between system design, software development, and programming are more apparent, even more so that developers become systems architects, those who design the multi-leveled architecture or component interactions of a large software system. In a large company, there may be employees whose sole responsibility consists of one of the phases above. In smaller development environments, a few people or even an individual might handle the complete process. The word software was coined as a prank as early as 1953, before this time, computers were programmed either by customers, or the few commercial computer vendors of the time, such as UNIVAC and IBM. The first company founded to provide products and services was Computer Usage Company in 1955. The software industry expanded in the early 1960s, almost immediately after computers were first sold in mass-produced quantities, universities, government, and business customers created a demand for software. Many of these programs were written in-house by full-time staff programmers, some were distributed freely between users of a particular machine for no charge. Others were done on a basis, and other firms such as Computer Sciences Corporation started to grow. The computer/hardware makers started bundling operating systems, systems software and programming environments with their machines, new software was built for microcomputers, so other manufacturers including IBM, followed DECs example quickly, resulting in the IBM AS/400 amongst others. The industry expanded greatly with the rise of the computer in the mid-1970s. In the following years, it created a growing market for games, applications. DOS, Microsofts first operating system product, was the dominant operating system at the time, by 2014 the role of cloud developer had been defined, in this context, one definition of a developer in general was published, Developers make software for the world to use. The job of a developer is to crank out code -- fresh code for new products, code fixes for maintenance, code for business logic, bus factor Software Developer description from the US Department of Labor
3.
Software release life cycle
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Usage of the alpha/beta test terminology originated at IBM. As long ago as the 1950s, IBM used similar terminology for their hardware development, a test was the verification of a new product before public announcement. B test was the verification before releasing the product to be manufactured, C test was the final test before general availability of the product. Martin Belsky, a manager on some of IBMs earlier software projects claimed to have invented the terminology, IBM dropped the alpha/beta terminology during the 1960s, but by then it had received fairly wide notice. The usage of beta test to refer to testing done by customers was not done in IBM, rather, IBM used the term field test. Pre-alpha refers to all activities performed during the project before formal testing. These activities can include requirements analysis, software design, software development, in typical open source development, there are several types of pre-alpha versions. Milestone versions include specific sets of functions and are released as soon as the functionality is complete, the alpha phase of the release life cycle is the first phase to begin software testing. In this phase, developers generally test the software using white-box techniques, additional validation is then performed using black-box or gray-box techniques, by another testing team. Moving to black-box testing inside the organization is known as alpha release, alpha software can be unstable and could cause crashes or data loss. Alpha software may not contain all of the features that are planned for the final version, in general, external availability of alpha software is uncommon in proprietary software, while open source software often has publicly available alpha versions. The alpha phase usually ends with a freeze, indicating that no more features will be added to the software. At this time, the software is said to be feature complete, Beta, named after the second letter of the Greek alphabet, is the software development phase following alpha. Software in the stage is also known as betaware. Beta phase generally begins when the software is complete but likely to contain a number of known or unknown bugs. Software in the phase will generally have many more bugs in it than completed software, as well as speed/performance issues. The focus of beta testing is reducing impacts to users, often incorporating usability testing, the process of delivering a beta version to the users is called beta release and this is typically the first time that the software is available outside of the organization that developed it. Beta version software is useful for demonstrations and previews within an organization
4.
Repository (version control)
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In revision control systems, a repository is an on-disk data structure which stores metadata for a set of files and/or directory structure. Some of the metadata that a repository contains includes, among other things, a set of references to commit objects, called heads. The main purpose of a repository is to store a set of files and these differences in methodology have generally led to diverse uses of revision control by different groups, depending on their needs. Software repository Codebase Forge Comparison of source code hosting facilities
5.
Operating system
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An operating system is system software that manages computer hardware and software resources and provides common services for computer programs. All computer programs, excluding firmware, require a system to function. Operating systems are found on many devices that contain a computer – from cellular phones, the dominant desktop operating system is Microsoft Windows with a market share of around 83. 3%. MacOS by Apple Inc. is in place, and the varieties of Linux is in third position. Linux distributions are dominant in the server and supercomputing sectors, other specialized classes of operating systems, such as embedded and real-time systems, exist for many applications. A single-tasking system can run one program at a time. Multi-tasking may be characterized in preemptive and co-operative types, in preemptive multitasking, the operating system slices the CPU time and dedicates a slot to each of the programs. Unix-like operating systems, e. g. Solaris, Linux, cooperative multitasking is achieved by relying on each process to provide time to the other processes in a defined manner. 16-bit versions of Microsoft Windows used cooperative multi-tasking, 32-bit versions of both Windows NT and Win9x, used preemptive multi-tasking. Single-user operating systems have no facilities to distinguish users, but may allow multiple programs to run in tandem, a distributed operating system manages a group of distinct computers and makes them appear to be a single computer. The development of networked computers that could be linked and communicate with each other gave rise to distributed computing, distributed computations are carried out on more than one machine. When computers in a work in cooperation, they form a distributed system. The technique is used both in virtualization and cloud computing management, and is common in large server warehouses, embedded operating systems are designed to be used in embedded computer systems. They are designed to operate on small machines like PDAs with less autonomy and they are able to operate with a limited number of resources. They are very compact and extremely efficient by design, Windows CE and Minix 3 are some examples of embedded operating systems. A real-time operating system is a system that guarantees to process events or data by a specific moment in time. A real-time operating system may be single- or multi-tasking, but when multitasking, early computers were built to perform a series of single tasks, like a calculator. Basic operating system features were developed in the 1950s, such as resident monitor functions that could run different programs in succession to speed up processing
6.
Computing platform
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Computing platform means in general sense, where any piece of software is executed. It may be the hardware or the system, even a web browser or other application. The term computing platform can refer to different abstraction levels, including a hardware architecture, an operating system. In total it can be said to be the stage on which programs can run. For example, an OS may be a platform that abstracts the underlying differences in hardware, platforms may also include, Hardware alone, in the case of small embedded systems. Embedded systems can access hardware directly, without an OS, this is referred to as running on bare metal, a browser in the case of web-based software. The browser itself runs on a platform, but this is not relevant to software running within the browser. An application, such as a spreadsheet or word processor, which hosts software written in a scripting language. This can be extended to writing fully-fledged applications with the Microsoft Office suite as a platform, software frameworks that provide ready-made functionality. Cloud computing and Platform as a Service, the social networking sites Twitter and facebook are also considered development platforms. A virtual machine such as the Java virtual machine, applications are compiled into a format similar to machine code, known as bytecode, which is then executed by the VM. A virtualized version of a system, including virtualized hardware, OS, software. These allow, for instance, a typical Windows program to run on what is physically a Mac, some architectures have multiple layers, with each layer acting as a platform to the one above it. In general, a component only has to be adapted to the layer immediately beneath it, however, the JVM, the layer beneath the application, does have to be built separately for each OS
7.
Java (software platform)
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Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. While they are less common than standalone Java applications, Java applets run in secure, sandboxed environments to provide many features of native applications, in addition, several languages have been designed to run natively on the JVM, including Scala, Clojure and Apache Groovy. Java syntax borrows heavily from C and C++, but object-oriented features are modeled after Smalltalk, Java eschews certain low-level constructs such as pointers and has a very simple memory model where every object is allocated on the heap and all variables of object types are references. Memory management is handled through integrated automatic garbage collection performed by the JVM, on November 13,2006, Sun Microsystems made the bulk of its implementation of Java available under the GNU General Public License. The latest version is Java 8, the only supported version as of 2016, Oracle has announced that using older versions of their JVM implementation presents serious risks due to unresolved security issues. The Java platform is a suite of programs that facilitate developing and running programs written in the Java programming language. A Java platform will include an engine, a compiler. Java ME, Specifies several different sets of libraries for devices with limited storage, display and it is often used to develop applications for mobile devices, PDAs, TV set-top boxes, and printers. Java SE, For general-purpose use on desktop PCs, servers, Java EE, Java SE plus various APIs which are useful for multi-tier client–server enterprise applications. The Java platform consists of programs, each of which provides a portion of its overall capabilities. For example, the Java compiler, which converts Java source code into Java bytecode, is provided as part of the Java Development Kit, the Java Runtime Environment, complementing the JVM with a just-in-time compiler, converts intermediate bytecode into native machine code on the fly. The Java platform also includes a set of libraries. The heart of the Java platform is the concept of a machine that executes Java bytecode programs. This bytecode is the same no matter what hardware or operating system the program is running under, there is a JIT compiler within the Java Virtual Machine, or JVM. The JIT compiler translates the Java bytecode into native processor instructions at run-time, the use of bytecode as an intermediate language permits Java programs to run on any platform that has a virtual machine available. Since JRE version 1.2, Suns JVM implementation has included a just-in-time compiler instead of an interpreter, although Java programs are cross-platform or platform independent, the code of the Java Virtual Machines that execute these programs is not. Every supported operating platform has its own JVM, in most modern operating systems, a large body of reusable code is provided to simplify the programmers job. This code is provided as a set of dynamically loadable libraries that applications can call at runtime
8.
Web browser
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A web browser is a software application for retrieving, presenting and traversing information resources on the World Wide Web. An information resource is identified by a Uniform Resource Identifier that may be a web page, image, hyperlinks present in resources enable users easily to navigate their browsers to related resources. Although browsers are primarily intended to use the World Wide Web, the most popular web browsers are Google Chrome, Microsoft Edge, Safari, Opera and Firefox. The first web browser was invented in 1990 by Sir Tim Berners-Lee, Berners-Lee is the director of the World Wide Web Consortium, which oversees the Webs continued development, and is also the founder of the World Wide Web Foundation. His browser was called WorldWideWeb and later renamed Nexus, the first commonly available web browser with a graphical user interface was Erwise. The development of Erwise was initiated by Robert Cailliau, andreesens browser sparked the internet boom of the 1990s. The introduction of Mosaic in 1993 – one of the first graphical web browsers – led to an explosion in web use, Microsoft responded with its Internet Explorer in 1995, also heavily influenced by Mosaic, initiating the industrys first browser war. Bundled with Windows, Internet Explorer gained dominance in the web browser market, Internet Explorer usage share peaked at over 95% by 2002. Opera debuted in 1996, it has never achieved widespread use and it is also available on several other embedded systems, including Nintendos Wii video game console. In 1998, Netscape launched what was to become the Mozilla Foundation in an attempt to produce a competitive browser using the open source software model, as of August 2011, Firefox has a 28% usage share. Apples Safari had its first beta release in January 2003, as of April 2011, the most recent major entrant to the browser market is Chrome, first released in September 2008. Chromes take-up has increased year by year, by doubling its usage share from 8% to 16% by August 2011. This increase seems largely to be at the expense of Internet Explorer, in December 2011, Chrome overtook Internet Explorer 8 as the most widely used web browser but still had lower usage than all versions of Internet Explorer combined. Chromes user-base continued to grow and in May 2012, Chromes usage passed the usage of all versions of Internet Explorer combined, by April 2014, Chromes usage had hit 45%. Internet Explorer was deprecated in Windows 10, with Microsoft Edge replacing it as the web browser. The ways that web browser makers fund their development costs has changed over time, the first web browser, WorldWideWeb, was a research project. In addition to being freeware, Netscape Navigator and Opera were also sold commercially, Internet Explorer, on the other hand, was bundled free with the Windows operating system, and therefore it was funded partly by the sales of Windows to computer manufacturers and direct to users. Internet Explorer also used to be available for the Mac, in this respect, IE may have contributed to Windows and Microsoft applications sales in another way, through lock-in to Microsofts browser
9.
Molecular modelling
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Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system, the common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling electrons of each atom, molecular mechanics is one aspect of molecular modelling, as it refers to the use of classical mechanics to describe the physical basis behind the models. Molecular models typically describe atoms as point charges with an associated mass, the interactions between neighbouring atoms are described by spring-like interactions and Van der Waals forces. The Lennard-Jones potential is used to describe the later. The electrostatic interactions are computed based on Coulombs law, atoms are assigned coordinates in Cartesian space or in internal coordinates, and can also be assigned velocities in dynamical simulations. The atomic velocities are related to the temperature of the system, the collective mathematical expression is termed a potential function and is related to the system internal energy, a thermodynamic quantity equal to the sum of potential and kinetic energies. Methods which minimize the energy are termed energy minimization methods. The set of parameters consisting of equilibrium bond lengths, bond angles, partial charge values, force constants, different implementations of molecular mechanics use different mathematical expressions and different parameters for the potential function. The common force fields in use today have developed by using high level quantum calculations and/or fitting to experimental data. The method, termed energy minimization, is used to find positions of zero gradient for all atoms, in other words, lower energy states are more stable and are commonly investigated because of their role in chemical and biological processes. A molecular dynamics simulation, on the hand, computes the behaviour of a system as a function of time. It involves solving Newtons laws of motion, principally the second law, integration of Newtons laws of motion, using different integration algorithms, leads to atomic trajectories in space and time. The force on an atom is defined as the gradient of the potential energy function. Molecules can be modelled either in vacuum, or in the presence of a solvent such as water, simulations of systems in vacuum are referred to as gas-phase simulations, while those that include the presence of solvent molecules are referred to as explicit solvent simulations. In another type of simulation, the effect of solvent is estimated using a mathematical expression. Most force fields are distance-dependent, making the most convenient expression for these Cartesian coordinates, in some fields the IC representation is termed the Z-matrix or torsion angle representation. Thus, it is common for computational optimizing programs to flip back
10.
Software license
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A software license is a legal instrument governing the use or redistribution of software. Under United States copyright law all software is copyright protected, in code as also object code form. The only exception is software in the public domain, most distributed software can be categorized according to its license type. Two common categories for software under copyright law, and therefore with licenses which grant the licensee specific rights, are proprietary software and free, unlicensed software outside the copyright protection is either public domain software or software which is non-distributed, non-licensed and handled as internal business trade secret. Contrary to popular belief, distributed unlicensed software is copyright protected. Examples for this are unauthorized software leaks or software projects which are placed on public software repositories like GitHub without specified license. As voluntarily handing software into the domain is problematic in some international law domains, there are also licenses granting PD-like rights. Therefore, the owner of a copy of software is legally entitled to use that copy of software. Hence, if the end-user of software is the owner of the respective copy, as many proprietary licenses only enumerate the rights that the user already has under 17 U. S. C. §117, and yet proclaim to take away from the user. Proprietary software licenses often proclaim to give software publishers more control over the way their software is used by keeping ownership of each copy of software with the software publisher. The form of the relationship if it is a lease or a purchase, for example UMG v. Augusto or Vernor v. Autodesk. The ownership of goods, like software applications and video games, is challenged by licensed. The Swiss based company UsedSoft innovated the resale of business software and this feature of proprietary software licenses means that certain rights regarding the software are reserved by the software publisher. Therefore, it is typical of EULAs to include terms which define the uses of the software, the most significant effect of this form of licensing is that, if ownership of the software remains with the software publisher, then the end-user must accept the software license. In other words, without acceptance of the license, the end-user may not use the software at all, one example of such a proprietary software license is the license for Microsoft Windows. The most common licensing models are per single user or per user in the appropriate volume discount level, Licensing per concurrent/floating user also occurs, where all users in a network have access to the program, but only a specific number at the same time. Another license model is licensing per dongle which allows the owner of the dongle to use the program on any computer, Licensing per server, CPU or points, regardless the number of users, is common practice as well as site or company licenses
11.
Software
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Computer software, or simply software, is that part of a computer system that consists of data or computer instructions, in contrast to the physical hardware from which the system is built. In computer science and software engineering, computer software is all information processed by computer systems, programs, computer software includes computer programs, libraries and related non-executable data, such as online documentation or digital media. Computer hardware and software require each other and neither can be used on its own. At the lowest level, executable code consists of machine language instructions specific to an individual processor—typically a central processing unit, a machine language consists of groups of binary values signifying processor instructions that change the state of the computer from its preceding state. For example, an instruction may change the value stored in a storage location in the computer—an effect that is not directly observable to the user. An instruction may also cause something to appear on a display of the computer system—a state change which should be visible to the user. The processor carries out the instructions in the order they are provided, unless it is instructed to jump to a different instruction, the majority of software is written in high-level programming languages that are easier and more efficient for programmers, meaning closer to a natural language. High-level languages are translated into machine language using a compiler or an interpreter or a combination of the two, an outline for what would have been the first piece of software was written by Ada Lovelace in the 19th century, for the planned Analytical Engine. However, neither the Analytical Engine nor any software for it were ever created, the first theory about software—prior to creation of computers as we know them today—was proposed by Alan Turing in his 1935 essay Computable numbers with an application to the Entscheidungsproblem. This eventually led to the creation of the academic fields of computer science and software engineering. Computer science is more theoretical, whereas software engineering focuses on practical concerns. However, prior to 1946, software as we now understand it—programs stored in the memory of stored-program digital computers—did not yet exist, the first electronic computing devices were instead rewired in order to reprogram them. On virtually all platforms, software can be grouped into a few broad categories. There are many different types of software, because the range of tasks that can be performed with a modern computer is so large—see list of software. System software includes, Operating systems, which are collections of software that manage resources and provides common services for other software that runs on top of them. Supervisory programs, boot loaders, shells and window systems are parts of operating systems. In practice, an operating system bundled with additional software so that a user can potentially do some work with a computer that only has an operating system. Device drivers, which operate or control a particular type of device that is attached to a computer, utilities, which are computer programs designed to assist users in the maintenance and care of their computers
12.
3D computer graphics
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Such images may be stored for viewing later or displayed in real-time. 3D computer graphics rely on many of the same algorithms as 2D computer vector graphics in the wire-frame model, 3D computer graphics are often referred to as 3D models. Apart from the graphic, the model is contained within the graphical data file. However, there are differences, a 3D model is the representation of any three-dimensional object. A model is not technically a graphic until it is displayed, a model can be displayed visually as a two-dimensional image through a process called 3D rendering or used in non-graphical computer simulations and calculations. With 3D printing, 3D models are rendered into a 3D physical representation of the model. William Fetter was credited with coining the term computer graphics in 1961 to describe his work at Boeing, 3D computer graphics software began appearing for home computers in the late 1970s. The earliest known example is 3D Art Graphics, a set of 3D computer graphics effects, written by Kazumasa Mitazawa, models can also be produced procedurally or via physical simulation. Basically, a 3D model is formed from points called vertices that define the shape, a polygon is an area formed from at least three vertexes. A polygon of n points is an n-gon, the overall integrity of the model and its suitability to use in animation depend on the structure of the polygons. Before rendering into an image, objects must be out in a scene. This defines spatial relationships between objects, including location and size, Animation refers to the temporal description of an object. These techniques are used in combination. As with animation, physical simulation also specifies motion, rendering converts a model into an image either by simulating light transport to get photo-realistic images, or by applying an art style as in non-photorealistic rendering. The two basic operations in realistic rendering are transport and scattering and this step is usually performed using 3D computer graphics software or a 3D graphics API. Altering the scene into a form for rendering also involves 3D projection. There are a multitude of websites designed to help, educate, some are managed by software developers and content providers, but there are standalone sites as well. These communities allow for members to seek advice, post tutorials, not all computer graphics that appear 3D are based on a wireframe model
13.
Molecule
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A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge, however, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions. In the kinetic theory of gases, the molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are in fact monoatomic molecules. A molecule may be homonuclear, that is, it consists of atoms of one element, as with oxygen, or it may be heteronuclear. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are not considered single molecules. Molecules as components of matter are common in organic substances and they also make up most of the oceans and atmosphere. Also, no typical molecule can be defined for ionic crystals and covalent crystals, the theme of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding, which means that solid metals are also not made of molecules. In glasses, atoms may also be together by chemical bonds with no presence of any definable molecule. The science of molecules is called molecular chemistry or molecular physics, in practice, however, this distinction is vague. In molecular sciences, a molecule consists of a system composed of two or more atoms. Polyatomic ions may sometimes be thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i. e, according to Merriam-Webster and the Online Etymology Dictionary, the word molecule derives from the Latin moles or small unit of mass. Molecule – extremely minute particle, from French molécule, from New Latin molecula, diminutive of Latin moles mass, a vague meaning at first, the vogue for the word can be traced to the philosophy of Descartes. The definition of the molecule has evolved as knowledge of the structure of molecules has increased, earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. Molecules are held together by covalent bonding or ionic bonding. Several types of non-metal elements exist only as molecules in the environment, for example, hydrogen only exists as hydrogen molecule. A molecule of a compound is made out of two or more elements, a covalent bond is a chemical bond that involves the sharing of electron pairs between atoms
14.
Chemistry
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Chemistry is a branch of physical science that studies the composition, structure, properties and change of matter. Chemistry is sometimes called the science because it bridges other natural sciences, including physics. For the differences between chemistry and physics see comparison of chemistry and physics, the history of chemistry can be traced to alchemy, which had been practiced for several millennia in various parts of the world. The word chemistry comes from alchemy, which referred to a set of practices that encompassed elements of chemistry, metallurgy, philosophy, astrology, astronomy, mysticism. An alchemist was called a chemist in popular speech, and later the suffix -ry was added to this to describe the art of the chemist as chemistry, the modern word alchemy in turn is derived from the Arabic word al-kīmīā. In origin, the term is borrowed from the Greek χημία or χημεία and this may have Egyptian origins since al-kīmīā is derived from the Greek χημία, which is in turn derived from the word Chemi or Kimi, which is the ancient name of Egypt in Egyptian. Alternately, al-kīmīā may derive from χημεία, meaning cast together, in retrospect, the definition of chemistry has changed over time, as new discoveries and theories add to the functionality of the science. The term chymistry, in the view of noted scientist Robert Boyle in 1661, in 1837, Jean-Baptiste Dumas considered the word chemistry to refer to the science concerned with the laws and effects of molecular forces. More recently, in 1998, Professor Raymond Chang broadened the definition of chemistry to mean the study of matter, early civilizations, such as the Egyptians Babylonians, Indians amassed practical knowledge concerning the arts of metallurgy, pottery and dyes, but didnt develop a systematic theory. Greek atomism dates back to 440 BC, arising in works by such as Democritus and Epicurus. In 50 BC, the Roman philosopher Lucretius expanded upon the theory in his book De rerum natura, unlike modern concepts of science, Greek atomism was purely philosophical in nature, with little concern for empirical observations and no concern for chemical experiments. Work, particularly the development of distillation, continued in the early Byzantine period with the most famous practitioner being the 4th century Greek-Egyptian Zosimos of Panopolis. He formulated Boyles law, rejected the four elements and proposed a mechanistic alternative of atoms. Before his work, though, many important discoveries had been made, the Scottish chemist Joseph Black and the Dutchman J. B. English scientist John Dalton proposed the theory of atoms, that all substances are composed of indivisible atoms of matter. Davy discovered nine new elements including the alkali metals by extracting them from their oxides with electric current, british William Prout first proposed ordering all the elements by their atomic weight as all atoms had a weight that was an exact multiple of the atomic weight of hydrogen. The inert gases, later called the noble gases were discovered by William Ramsay in collaboration with Lord Rayleigh at the end of the century, thereby filling in the basic structure of the table. Organic chemistry was developed by Justus von Liebig and others, following Friedrich Wöhlers synthesis of urea which proved that organisms were, in theory
15.
Biochemistry
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Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through biochemical signaling and the flow of energy through metabolism. Biochemistry is closely related to biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Depending on the definition of the terms used, molecular biology can be thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate. The chemistry of the cell depends on the reactions of smaller molecules. These can be inorganic, for water and metal ions, or organic, for example the amino acids. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism, the findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases, in nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control. However, biochemistry as a scientific discipline has its beginning sometime in the 19th century, or a little earlier. Gowland Hopkins on enzymes and the nature of biochemistry. The term biochemistry itself is derived from a combination of biology, the German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister. Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea and these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle. Another significant historic event in biochemistry is the discovery of the gene and this part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, in 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92 naturally occurring elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life, while a few common ones are not used, most organisms share element needs, but there are a few differences between plants and animals
16.
Microsoft Windows
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Microsoft Windows is a metafamily of graphical operating systems developed, marketed, and sold by Microsoft. It consists of families of operating systems, each of which cater to a certain sector of the computing industry with the OS typically associated with IBM PC compatible architecture. Active Windows families include Windows NT, Windows Embedded and Windows Phone, defunct Windows families include Windows 9x, Windows 10 Mobile is an active product, unrelated to the defunct family Windows Mobile. Microsoft introduced an operating environment named Windows on November 20,1985, Microsoft Windows came to dominate the worlds personal computer market with over 90% market share, overtaking Mac OS, which had been introduced in 1984. Apple came to see Windows as an encroachment on their innovation in GUI development as implemented on products such as the Lisa. On PCs, Windows is still the most popular operating system, however, in 2014, Microsoft admitted losing the majority of the overall operating system market to Android, because of the massive growth in sales of Android smartphones. In 2014, the number of Windows devices sold was less than 25% that of Android devices sold and this comparison however may not be fully relevant, as the two operating systems traditionally target different platforms. As of September 2016, the most recent version of Windows for PCs, tablets, smartphones, the most recent versions for server computers is Windows Server 2016. A specialized version of Windows runs on the Xbox One game console, Microsoft, the developer of Windows, has registered several trademarks each of which denote a family of Windows operating systems that target a specific sector of the computing industry. It now consists of three operating system subfamilies that are released almost at the time and share the same kernel. Windows, The operating system for personal computers, tablets. The latest version is Windows 10, the main competitor of this family is macOS by Apple Inc. for personal computers and Android for mobile devices. Windows Server, The operating system for server computers, the latest version is Windows Server 2016. Unlike its clients sibling, it has adopted a strong naming scheme, the main competitor of this family is Linux. Windows PE, A lightweight version of its Windows sibling meant to operate as an operating system, used for installing Windows on bare-metal computers. The latest version is Windows PE10.0.10586.0, Windows Embedded, Initially, Microsoft developed Windows CE as a general-purpose operating system for every device that was too resource-limited to be called a full-fledged computer. The following Windows families are no longer being developed, Windows 9x, Microsoft now caters to the consumers market with Windows NT. Windows Mobile, The predecessor to Windows Phone, it was a mobile operating system
17.
MacOS
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Within the market of desktop, laptop and home computers, and by web usage, it is the second most widely used desktop OS after Microsoft Windows. Launched in 2001 as Mac OS X, the series is the latest in the family of Macintosh operating systems, Mac OS X succeeded classic Mac OS, which was introduced in 1984, and the final release of which was Mac OS9 in 1999. An initial, early version of the system, Mac OS X Server 1.0, was released in 1999, the first desktop version, Mac OS X10.0, followed in March 2001. In 2012, Apple rebranded Mac OS X to OS X. Releases were code named after big cats from the release up until OS X10.8 Mountain Lion. Beginning in 2013 with OS X10.9 Mavericks, releases have been named after landmarks in California, in 2016, Apple rebranded OS X to macOS, adopting the nomenclature that it uses for their other operating systems, iOS, watchOS, and tvOS. The latest version of macOS is macOS10.12 Sierra, macOS is based on technologies developed at NeXT between 1985 and 1997, when Apple acquired the company. The X in Mac OS X and OS X is pronounced ten, macOS shares its Unix-based core, named Darwin, and many of its frameworks with iOS, tvOS and watchOS. A heavily modified version of Mac OS X10.4 Tiger was used for the first-generation Apple TV, Apple also used to have a separate line of releases of Mac OS X designed for servers. Beginning with Mac OS X10.7 Lion, the functions were made available as a separate package on the Mac App Store. Releases of Mac OS X from 1999 to 2005 can run only on the PowerPC-based Macs from the time period, Mac OS X10.5 Leopard was released as a Universal binary, meaning the installer disc supported both Intel and PowerPC processors. In 2009, Apple released Mac OS X10.6 Snow Leopard, in 2011, Apple released Mac OS X10.7 Lion, which no longer supported 32-bit Intel processors and also did not include Rosetta. All versions of the system released since then run exclusively on 64-bit Intel CPUs, the heritage of what would become macOS had originated at NeXT, a company founded by Steve Jobs following his departure from Apple in 1985. There, the Unix-like NeXTSTEP operating system was developed, and then launched in 1989 and its graphical user interface was built on top of an object-oriented GUI toolkit using the Objective-C programming language. This led Apple to purchase NeXT in 1996, allowing NeXTSTEP, then called OPENSTEP, previous Macintosh operating systems were named using Arabic numerals, e. g. Mac OS8 and Mac OS9. The letter X in Mac OS Xs name refers to the number 10 and it is therefore correctly pronounced ten /ˈtɛn/ in this context. However, a common mispronunciation is X /ˈɛks/, consumer releases of Mac OS X included more backward compatibility. Mac OS applications could be rewritten to run natively via the Carbon API, the consumer version of Mac OS X was launched in 2001 with Mac OS X10.0. Reviews were variable, with praise for its sophisticated, glossy Aqua interface
18.
Linux
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Linux is a Unix-like computer operating system assembled under the model of free and open-source software development and distribution. The defining component of Linux is the Linux kernel, an operating system kernel first released on September 17,1991 by Linus Torvalds, the Free Software Foundation uses the name GNU/Linux to describe the operating system, which has led to some controversy. Linux was originally developed for computers based on the Intel x86 architecture. Because of the dominance of Android on smartphones, Linux has the largest installed base of all operating systems. Linux is also the operating system on servers and other big iron systems such as mainframe computers. It is used by around 2. 3% of desktop computers, the Chromebook, which runs on Chrome OS, dominates the US K–12 education market and represents nearly 20% of the sub-$300 notebook sales in the US. Linux also runs on embedded systems – devices whose operating system is built into the firmware and is highly tailored to the system. This includes TiVo and similar DVR devices, network routers, facility automation controls, televisions, many smartphones and tablet computers run Android and other Linux derivatives. The development of Linux is one of the most prominent examples of free, the underlying source code may be used, modified and distributed—commercially or non-commercially—by anyone under the terms of its respective licenses, such as the GNU General Public License. Typically, Linux is packaged in a known as a Linux distribution for both desktop and server use. Distributions intended to run on servers may omit all graphical environments from the standard install, because Linux is freely redistributable, anyone may create a distribution for any intended use. The Unix operating system was conceived and implemented in 1969 at AT&Ts Bell Laboratories in the United States by Ken Thompson, Dennis Ritchie, Douglas McIlroy, first released in 1971, Unix was written entirely in assembly language, as was common practice at the time. Later, in a key pioneering approach in 1973, it was rewritten in the C programming language by Dennis Ritchie, the availability of a high-level language implementation of Unix made its porting to different computer platforms easier. Due to an earlier antitrust case forbidding it from entering the computer business, as a result, Unix grew quickly and became widely adopted by academic institutions and businesses. In 1984, AT&T divested itself of Bell Labs, freed of the legal obligation requiring free licensing, the GNU Project, started in 1983 by Richard Stallman, has the goal of creating a complete Unix-compatible software system composed entirely of free software. Later, in 1985, Stallman started the Free Software Foundation, by the early 1990s, many of the programs required in an operating system were completed, although low-level elements such as device drivers, daemons, and the kernel were stalled and incomplete. Linus Torvalds has stated that if the GNU kernel had been available at the time, although not released until 1992 due to legal complications, development of 386BSD, from which NetBSD, OpenBSD and FreeBSD descended, predated that of Linux. Torvalds has also stated that if 386BSD had been available at the time, although the complete source code of MINIX was freely available, the licensing terms prevented it from being free software until the licensing changed in April 2000
19.
Unix
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Among these is Apples macOS, which is the Unix version with the largest installed base as of 2014. Many Unix-like operating systems have arisen over the years, of which Linux is the most popular, Unix was originally meant to be a convenient platform for programmers developing software to be run on it and on other systems, rather than for non-programmer users. The system grew larger as the system started spreading in academic circles, as users added their own tools to the system. Unix was designed to be portable, multi-tasking and multi-user in a time-sharing configuration and these concepts are collectively known as the Unix philosophy. By the early 1980s users began seeing Unix as a universal operating system. Under Unix, the system consists of many utilities along with the master control program. To mediate such access, the kernel has special rights, reflected in the division between user space and kernel space, the microkernel concept was introduced in an effort to reverse the trend towards larger kernels and return to a system in which most tasks were completed by smaller utilities. In an era when a standard computer consisted of a disk for storage and a data terminal for input and output. However, modern systems include networking and other new devices, as graphical user interfaces developed, the file model proved inadequate to the task of handling asynchronous events such as those generated by a mouse. In the 1980s, non-blocking I/O and the set of inter-process communication mechanisms were augmented with Unix domain sockets, shared memory, message queues, and semaphores. In microkernel implementations, functions such as network protocols could be moved out of the kernel, Multics introduced many innovations, but had many problems. Frustrated by the size and complexity of Multics but not by the aims and their last researchers to leave Multics, Ken Thompson, Dennis Ritchie, M. D. McIlroy, and J. F. Ossanna, decided to redo the work on a much smaller scale. The name Unics, a pun on Multics, was suggested for the project in 1970. Peter H. Salus credits Peter Neumann with the pun, while Brian Kernighan claims the coining for himself, in 1972, Unix was rewritten in the C programming language. Bell Labs produced several versions of Unix that are referred to as Research Unix. In 1975, the first source license for UNIX was sold to faculty at the University of Illinois Department of Computer Science, UIUC graduate student Greg Chesson was instrumental in negotiating the terms of this license. During the late 1970s and early 1980s, the influence of Unix in academic circles led to adoption of Unix by commercial startups, including Sequent, HP-UX, Solaris, AIX. In the late 1980s, AT&T Unix System Laboratories and Sun Microsystems developed System V Release 4, in the 1990s, Unix-like systems grew in popularity as Linux and BSD distributions were developed through collaboration by a worldwide network of programmers
20.
Free and open-source software
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Free and open-source software is computer software that can be classified as both free software and open-source software. This is in contrast to proprietary software, where the software is under restrictive copyright, the benefits of using FOSS can include decreasing software costs, increasing security and stability, protecting privacy, and giving users more control over their own hardware. Free, open-source operating systems such as Linux and descendents of BSD are widely utilized today, powering millions of servers, desktops, smartphones, Free software licenses and open-source licenses are used by many software packages. In the 1950s, 1960s, and 1970s to 1980s, it was common for users to have the source code for all programs they used. Software, including source code, was shared by individuals who used computers. Most companies had a model based on hardware sales, and provided or bundled software with hardware. Organizations of users and suppliers were formed to facilitate the exchange of software, see, for example, SHARE, by the late 1960s, the prevailing business model around software was changing. In United States vs. IBM, filed 17 January 1969, while some software might always be free, there would be a growing amount of software that was for sale only. Software development for the GNU operating system began in January 1984, an article outlining the project and its goals was published in March 1985 titled the GNU Manifesto. The manifesto included significant explanation of the GNU philosophy, Free Software Definition, the Linux kernel, started by Linus Torvalds, was released as freely modifiable source code in 1991. Initially, Linux was not released under a free or open-source software license, however, with version 0.12 in February 1992, he relicensed the project under the GNU General Public License. Much like Unix, Torvalds kernel attracted the attention of volunteer programmers, freeBSD and NetBSD were released as free software when the USL v. BSDi lawsuit was settled out of court in 1993. OpenBSD forked from NetBSD in 1995, also in 1995, The Apache HTTP Server, commonly referred to as Apache, was released under the Apache License 1.0. In 1997, Eric Raymond published The Cathedral and the Bazaar and this code is today better known as Mozilla Firefox and Thunderbird. Netscapes act prompted Raymond and others to look into how to bring the FSFs free software ideas, the new name they chose was open source, and quickly Bruce Perens, publisher Tim OReilly, Linus Torvalds, and others signed on to the rebranding. The Open Source Initiative was founded in February 1998 to encourage use of the new term, a Microsoft executive publicly stated in 2001 that open source is an intellectual property destroyer. I cant imagine something that could be worse than this for the software business and this view perfectly summarizes the initial response to FOSS by some software corporations. IBM, Oracle, Google and State Farm are just a few of the companies with a serious public stake in todays competitive open-source market, there has been a significant shift in the corporate philosophy concerning the development of free and open-source software
21.
Apache Taverna
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The set of available services is not finite and users can import new service descriptions into the Taverna Workbench. Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows, the Taverna workflow engine is also available separately, as a Java API, command line tool or as a server. Taverna is used by users in many domains, such as bioinformatics, cheminformatics, medicine, astronomy, social science, music, and digital preservation. Some of the services for the use in Taverna workflows can be discovered through the BioCatalogue - a public, Taverna workflows can also be shared with other people through the myExperiment social web site for scientists. BioCatalogue and myExperiment are another two product from the myGrid consortium, Taverna is used in over 350 organizations around the world, both academic and commercial. As of 2011, there have been over 80,000 downloads of Taverna across different versions, Taverna workflows can invoke general SOAP/WSDL or REST Web services, and more specific SADI, BioMart, BioMoby and SoapLab Web services. It can also invoke R statistical services, local Java code, external tools on local and remote machines, do XPath and other manipulation, import a spreadsheet. Taverna includes the ability to search for services described in BioCatalogue to invoke from workflows, however, services do not need to be described within BioCatalogue to be included in workflows as they can be added from a WSDL Web Service description or entered as a REST URI pattern. Taverna also includes the capability to search for workflows on myExperiment, the Taverna Workbench can download, modify and run workflows discovered on myExperiment, and also upload created workflows in order to share them with others using the social aspects of myExperiment. Taverna workflows do not need to be executed within the Taverna Workbench, Taverna services execute in parallel when possible, as Taverna workflows are primarily data-driven rather than control-driven. Taverna has been a project since 2003, with contributors from multiple academic. In 2014-10, Taverna became an independent Apache incubator project, the project is developing Apache Taverna 3. x, which license change from LGPL2.1 to Apache License 2.0. Apache Taverna at the Apache incubator Taverna homepage
22.
Ball-and-stick model
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In chemistry, the ball-and-stick model is a molecular model of a chemical substance which is to display both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods which represent the bonds, double and triple bonds are usually represented by two or three curved rods, respectively. The chemical element of each atom is often indicated by the spheres color, in a ball-and-stick model, the radius of the spheres is usually much smaller than the rod lengths, in order to provide a clearer view of the atoms and bonds throughout the model. As a consequence, the model does not provide an insight about the space occupied by the model. Ball-and-stick models can be physical artifacts or virtual computer models, the former are usually built from molecular modeling kits, consisting of a number of helical springs or rods made of flexible plastic, and a number of plastic balls with pre-drilled holes. The sphere colors commonly follow the CPK coloring, some university courses on chemistry require students to buy such models as learning material. In 1865, German chemist August Wilhelm von Hofmann was the first to make stick-and-ball molecular models and he used such models in lecture at the Royal Institution of Great Britain. Specialist companies manufacture kits and models to order, one of the earlier companies was Woosters at Bottisham, Cambridgeshire, UK. Besides tetrahedral, trigonal and octahedral holes, there were all-purpose balls with 24 holes and these models allowed rotation about the single rod bonds, which could be both an advantage and a disadvantage. The approximate scale was 5 cm per ångström, but was not consistent over all elements, the Beevers Miniature Models company in Edinburgh produced small models using PMMA balls and stainless steel rods. In these models, the use of individually drilled balls with precise bond angles and bond lengths enabled large crystal structures to be created in a light. Figure 3 shows a cell of ruby in this style
23.
Space-filling model
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Atoms of different chemical elements are usually represented by spheres of different colors. They are distinguished from other 3D representations, such as the ball-and-stick and skeletal models and they are useful for visualizing the effective shape and relative dimensions of the molecule, and the shapes of surface a given static conformer might present. For this reason, such models are of greater utility if they can be used dynamically, especially used with complex molecules. Space-filling models arise out of a desire to represent molecules in ways that reflect the electronic surfaces that molecules present, in short, for reasons of utility, crystallographic data historically have appeared in presentations closer to ball-and-stick models. In 1952, Robert Corey and Linus Pauling described accurate scale models of molecules which they had built at Caltech, a connector was designed—a metal bushing that threaded into each sphere at the center of each flat face. The two spheres were then held together by a metal rod inserted into the pair of opposing bushing. The models also had special features to allow representation of hydrogen bonds, such colour-coded, bond length-defined, van der Waals-type space-filling models are now commonly known as CPK models, after these three developers of the specific concept. The two closing images give examples of the type of calculation and representation, and its utility. Van der Waals surface CPK coloring Molecular graphics Software for molecular modeling Molecular design software More on molecular models and a couple of examples from chemistry and biology
24.
Ribbon diagram
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Ribbon diagrams, also known as Richardson Diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone, α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and lines or thin tubes for non-repetitive coils or loops. The direction of the chain is shown locally by the arrows. Ribbon diagrams are simple, yet powerful, in expressing the visual basics of a molecular structure, as well as the TIM ribbon drawing at the right, other hand-drawn examples are for prealbumin, flavodoxin, and Cu, Zn superoxide dismutase. In 1982, Arthur M. Lesk and co-workers first enabled automatic generation of ribbon diagrams through an implementation that uses Protein Data Bank files as input. This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes, most modern graphics systems provide either B-splines or Hermite splines as a basic drawing primitive. One type of spline implementation passes through each Cα guide point, producing an exact, both hand-drawn and most computer ribbons are smoothed over about 4 successive guide points, to produce a more visually pleasing and understandable representation. One popular program used for drawing ribbon diagrams is Molscript, Molscript utilizes Hermite splines to create coordinates for coils, turns, strands and helices. The curve passes through all its control points guided by direction vectors, the program was built on the basis of traditional molecular graphics by Arthur M. Lesk, Karl Hardman, and John Priestle. Jmol is an open-source Java-based viewer for browsing molecular structures on the web, other graphics programs such as DeepView and MolMol also produce ribbon images. KiNG is the Java-based successor to Mage
25.
JavaScript
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JavaScript is a high-level, dynamic, untyped, and interpreted programming language. It has been standardized in the ECMAScript language specification, JavaScript is prototype-based with first-class functions, making it a multi-paradigm language, supporting object-oriented, imperative, and functional programming styles. JavaScript was influenced by programming languages such as Self and Scheme, JavaScript is also used in environments that are not Web-based, such as PDF documents, site-specific browsers, and desktop widgets. Newer and faster JavaScript virtual machines and platforms built upon them have increased the popularity of JavaScript for server-side Web applications. On the client side, developers have traditionally implemented JavaScript as an interpreted language, programmers also use JavaScript in video-game development, in crafting desktop and mobile applications, and in server-side network programming with run-time environments such as Node. js. In 1994, a company called Mosaic Communications was founded in Mountain View, California, however, it intentionally shared no code with NCSA Mosaic. The internal codename for the browser was Mozilla, which stood for Mosaic killer. The first version of the Web browser, Mosaic Netscape 0.9, was released in late 1994, within four months it had already taken three-quarters of the browser market and became the main browser for Internet in the 1990s. To avoid trademark problems with the NCSA, the browser was subsequently renamed Netscape Navigator in the same year. Netscape Communications realized that the Web needed to more dynamic. In 1995, the company recruited Brendan Eich with the goal of embedding the Scheme programming language into its Netscape Navigator, to defend the idea of JavaScript against competing proposals, the company needed a prototype. Eich wrote one in 10 days, in May 1995, there is a common misconception that JavaScript was influenced by an earlier Web page scripting language developed by Nombas named C--. Brendan Eich, however, had never heard of C-- before he created LiveScript, Nombas did pitch their embedded Web page scripting to Netscape, though Web page scripting was not a new concept, as shown by the ViolaWWW Web browser. Nombas later switched to offering JavaScript instead of C-- in their ScriptEase product and was part of the TC39 group that standardized ECMAScript, in December 1995, soon after releasing JavaScript for browsers, Netscape introduced an implementation of the language for server-side scripting with Netscape Enterprise Server. Since the mid-2000s, additional server-side JavaScript implementations have been introduced, Microsoft script technologies including VBScript and JScript were released in 1996. JScript, an implementation of Netscapes JavaScript, was part of Internet Explorer 3. JScript was also available for server-side scripting in Internet Information Server, JavaScript began to acquire a reputation for being one of the roadblocks to a cross-platform and standards-driven Web. Some developers took on the task of trying to make their sites work in both major browsers, but many could not afford the time
26.
HTML5
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HTML5 is a markup language used for structuring and presenting content on the World Wide Web. It is the fifth and current version of the HTML standard, HTML5 is intended to subsume not only HTML4, but also XHTML1 and DOM Level 2 HTML. For the same reasons, HTML5 is also a candidate for cross-platform mobile applications, many new syntactic features are included. To enrich the content of documents, new page structure elements such as <main>, <section>, <article>, <header>, <footer>, <aside>, <nav>. New attributes are introduced, some elements and attributes have been removed, the APIs and Document Object Model are now fundamental parts of the HTML5 specification and HTML5 also better defines the processing for any invalid documents. The Web Hypertext Application Technology Working Group began work on the new standard in 2004, at that time, HTML4.01 had not been updated since 2000, and the World Wide Web Consortium was focusing future developments on XHTML2.0. In 2009, the W3C allowed the XHTML2.0 Working Groups charter to expire, W3C and WHATWG are currently working together on the development of HTML5.0. The workshop concluded with a vote—8 for,14 against—for continuing work on HTML, the two specifications were later merged to form HTML5. The HTML5 specification was adopted as the point of the work of the new HTML working group of the W3C in 2007. WHATWG published the First Public Working Draft of the specification on 22 January 2008, while some features of HTML5 are often compared to Adobe Flash, the two technologies are very different. Both include features for playing audio and video within web pages, however, HTML5 on its own cannot be used for animation or interactivity – it must be supplemented with CSS3 or JavaScript. There are many Flash capabilities that have no counterpart in HTML5. See Comparison of HTML5 and Flash, in early November 2011, Adobe announced that it would discontinue development of Flash for mobile devices and reorient its efforts in developing tools using HTML5. On 14 February 2011, the W3C extended the charter of its HTML Working Group with clear milestones for HTML5, in May 2011, the working group advanced HTML5 to Last Call, an invitation to communities inside and outside W3C to confirm the technical soundness of the specification. The W3C developed a comprehensive test suite to achieve broad interoperability for the specification by 2014. In January 2011, the WHATWG renamed its HTML5 living standard to HTML, the W3C nevertheless continued its project to release HTML5. In July 2012, WHATWG and W3C decided on a degree of separation, W3C will continue the HTML5 specification work, focusing on a single definitive standard, which is considered as a snapshot by WHATWG. The WHATWG organization will continue its work with HTML5 as a Living Standard, the concept of a living standard is that it is never complete and is always being updated and improved
27.
Plug-in (computing)
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In computing, a plug-in is a software component that adds a specific feature to an existing computer program. When a program supports plug-ins, it enables customization, the common examples are the plug-ins used in web browsers to add new features such as search-engines, virus scanners, or the ability to use a new file type such as a new video format. Applications support plug-ins for many reasons, types of applications and why they use plug-ins, Audio editors use plug-ins to generate, process or analyse sound. Ardour and Audacity are examples of such editors, email clients use plug-ins to decrypt and encrypt email. Pretty Good Privacy is an example of such plug-ins, graphics software use plug-ins to support file formats and process images. Media players use plug-ins to support file formats and apply filters, foobar2000, GStreamer, Quintessential, VST, Winamp, XMMS are examples of such media players. Packet sniffers use plug-ins to decode packet formats, omniPeek is an example of such packet sniffers. Remote sensing applications use plug-ins to process data from different sensor types, Visual Studio itself can be plugged into other applications via Visual Studio Tools for Office and Visual Studio Tools for Applications. Web browsers use browser extensions to expand their functionality, examples include Adobe Flash Player, Java SE, QuickTime, Microsoft Silverlight and Unity. The host application provides services which the plug-in can use, including a way for plug-ins to register themselves with the host application, plug-ins depend on the services provided by the host application and do not usually work by themselves. Programmers typically implement plug-in functionality using shared libraries installed in a place prescribed by the host application, HyperCard supported a similar facility, but more commonly included the plug-in code in the HyperCard documents themselves. Thus the HyperCard stack became a self-contained application in its own right, programs may also implement plugins by loading a directory of simple script files written in a scripting language like Python or Lua. In Mozilla Foundation definitions, the words add-on, extension and plug-in are not synonyms, add-on can refer to anything that extends the functions of a Mozilla application. Extensions comprise a subtype, albeit the most common and the most powerful one, Mozilla applications come with integrated add-on managers that, similar to package managers, install, update and manage extensions. The term, Plug-in, however, strictly refers to NPAPI-based web content renderers, the plug-in program could make calls to the editor to have it perform text-editing services upon the buffer that the editor shared with the plug-in. The Waterloo Fortran compiler used this feature to allow interactive compilation of Fortran programs edited by EDT, very early PC software applications to incorporate plug-in functionality included HyperCard and QuarkXPress on the Macintosh, both released in 1987. In 1988, Silicon Beach Software included plug-in functionality in Digital Darkroom and SuperPaint, and Ed Bomke coined the term plug-in
28.
Internet Explorer
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Internet Explorer is a discontinued series of graphical web browsers developed by Microsoft and included as part of the Microsoft Windows line of operating systems, starting in 1995. It was first released as part of the add-on package Plus. for Windows 95 that year, later versions were available as free downloads, or in service packs, and included in the original equipment manufacturer service releases of Windows 95 and later versions of Windows. Internet Explorer was one of the most widely used web browsers and this came after Microsoft used bundling to win the first browser war against Netscape, which was the dominant browser in the 1990s. Estimates for Internet Explorers overall market share range from 5. 45% to 27. 38% or by StatCounters numbers ranked 3rd, just after Firefox, as of August 2016. Microsoft spent over US$100 million per year on Internet Explorer in the late 1990s, on March 17,2015, Microsoft announced that Microsoft Edge would replace Internet Explorer as the default browser on its Windows 10 devices. This effectively makes Internet Explorer 11 the last release, Internet Explorer will, however, remain on some versions of Windows 10 primarily for enterprise purposes. Starting January 12,2016, only Internet Explorer 11 is supported with more security than older versions, support varies based on the operating systems technical capabilities and its support lifecycle. The Internet Explorer project was started in the summer of 1994 by Thomas Reardon, Mosaic, which was an early commercial web browser with formal ties to the pioneering National Center for Supercomputing Applications Mosaic browser. In late 1994, Microsoft licensed Spyglass Mosaic for a fee plus a percentage of Microsofts non-Windows revenues for the software. Although bearing a similar to NCSA Mosaic, Spyglass Mosaic had used the NCSA Mosaic source code sparingly. Microsoft was sued by Synet Inc. in 1996, over the trademark infringement, the first version of Internet Explorer, Microsoft Internet Explorer made its debut on August 16,1995. It was a version of Spyglass Mosaic, which Microsoft licensed from Spyglass Inc. like many other companies initiating browser development. It was installed as part of the Internet Jumpstart Kit in Microsoft Plus. for Windows 95, the Internet Explorer team began with about six people in early development. Internet Explorer 1.5 was released months later for Windows NT. By including it free of charge on their system, they did not have to pay royalties to Spyglass Inc, resulting in a lawsuit. Windows Internet Explorer 9 was released on March 14,2011, development for Internet Explorer 9 began shortly after the release of Internet Explorer 8. At MIX10, Microsoft showed and publicly released the first Platform Preview for Internet Explorer 9, ultimately, eight platform previews were released. The first public beta was released at an event in San Francisco
29.
Firefox 2
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Mozilla Firefox 2 is a version of Firefox, a web browser released on October 24,2006 by the Mozilla Corporation. Firefox 2 uses version 1.8 of the Gecko layout engine for displaying web pages, the release contained many new features not found in Firefox 1.5, including improved support for Scalable Vector Graphics and JavaScript 1.7, as well as user interface changes. On March 22,2006, the first alpha version of Firefox 2 was released and it featured Gecko 1.8.1 for the first time. Mozilla Firefox 2.0.0. x is the version officially supported on Windows NT4.0 and Windows 98. Mac OS X10.5 support was added October 18,2007 with version 2.0.0.8, Mozilla ended support for Firefox 2 on December 18,2008. Links default to open in new tab, inline spell checking for text boxes. Session restoration after a browser crash, search suggestion for Google and Yahoo. New search plugin manager and add-on manager, support for SVG text using svg, textPath. Search suggestions appear with search history in the box for Google. Support for client-side session and persistent storage, enhanced security and localization support for extensions. Internet Explorer 7 had climbed to 3. 18%, while Firefox 2.0 was at 0. 69%, a Softpedia article, however, noted in July 2007 that Firefox 2.0 has been also expanding its share constantly in spite of IE7. From just 0. 69% in October 2006, Firefox 2.0 is now accounting for 11. 07% of the market, Mozilla has even sacrificed version 1.5 of its open source browser for Firefox 2.0. With support cut at the end of June, Firefox 1.5 dropped to just 2. 85%, Firefox 2 began to lose notable market share to Firefox 3. Within 24 hours after its release, Firefox 3 usage rose from under 1% to over 3% according to Net Applications in that time period, Firefox 2. x was end-of-lifed in December,2008. With roughly 26 months of support, only Firefox 3.6 was supported longer, the Gecko 1.8.1 browser core continued to receive patches for projects such as Camino, K-Meleon, and SeaMonkey, even after official Firefox releases had ceased. By 2011, the 1.8.1 core had become obsolete, as major websites dropped support for it by employing newer technologies for presentation and complex scripting. The latter can be resource-intensive with the core, and users stuck with it should use NoScript to avoid issues with scripts that take too long to process. Mozilla Firefox homepage for end-users Mozilla Firefox project page for developers Mozilla EULA Firefox 2 at DMOZ
30.
Mac OS 9
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Mac OS9 is the ninth and final major release of Apples classic Mac OS operating system. While Mac OS9 lacks protected memory and full pre-emptive multitasking, lasting improvements include the introduction of an automated Software Update engine, Apple discontinued development of Mac OS9 in 2001, transitioning all future development to macOS, then named Mac OS X. Since that time, no updates have been released, the final updates to Mac OS9 addressed compatibility issues with macOS while running in the Classic Environment and compatibility with Carbon applications. At the 2002 World Wide Developers Conference, Steve Jobs began his address by staging a mock funeral for OS9. Mac OS9 also featured integrated support for Apple’s suite of Internet services known as iTools, other features new to Mac OS9 include, Integrated support for multiple user accounts without using At Ease. Support for voice login through VoicePrint passwords, keychain, a feature allowing users to save passwords and textual data encrypted in protected keychains. A Software Update control panel for automatic download and installation of Apple system software updates, a redesigned Sound control panel and support for USB audio. Speakable Items 2.0, also known as PlainTalk, featuring improved speech synthesis, remote Access Personal Server 3.5, including support for TCP/IP clients over Point-to-Point Protocol. An updated version of AppleScript with support for TCP/IP, USB Printer Sharing, a control panel allowing certain USB printers to be shared across a TCP/IP network. 128-bit file encryption in the Finder, support for files larger than 2 GB. This is achieved through running Mac OS9 without access to Finder inside OS X and this requires Mac OS9 to be installed on the computer, even if computers that can run the Classic environment are not necessarily able to boot into Mac OS9. Some Mac OS9 applications do not run well in Classic and they demonstrate screen redraw problems and lagging performance. In addition, some drivers and other software directly interact with the hardware fail to work properly. In May 2002, at Apples Worldwide Developers Conference in San Jose, California, Steve Jobs, accompanied by a coffin, Mac OS9.2.2, released in December 2001, was the final version of Mac OS9 and the classic Mac OS. In June 2005, Jobs announced that the Macintosh platform would be transitioning to Intel x86 microprocessors, developer documentation of the Rosetta PowerPC emulation layer revealed that applications written for Mac OS8 or 9 would not run on x86-based Macs. The Classic Environment remains in the PowerPC version of OS X10.4, however, as a workaround for Intel-based Macs, Mac OS9 can be emulated up to version 9.0.4 by using SheepShaver, a PowerPC emulator. It cannot emulate above 9.0.4 because SheepShaver does not emulate a memory management unit, the PearPC PowerPC emulator does not support Mac OS9. While Mac OS9 is no longer supported by Apple, retail copies are available from several Internet businesses at varying prices
31.
Firefox
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Mozilla Firefox is a free and open-source web browser developed by the Mozilla Foundation and its subsidiary the Mozilla Corporation. Firefox was created in 2002, under the name Phoenix by the Mozilla community members who wanted a standalone rather than the Mozilla Application Suite bundle. Even during its phase, Firefox proved to be popular with its testers and was praised for its speed, security. Firefox was released in November 2004, and was successful with 60 million downloads within nine months. Firefox is considered the successor of Netscape Navigator, as the Mozilla community was created by Netscape in 1998 before their acquisition by AOL. Firefox usage grew to a peak of 32% at the end of 2009, usage then declined in competition with Google Chrome. As of January 2016, Firefox has between 9% and 16% of worldwide usage as a browser, making it the second most popular web browser. Firefox is still the most popular browser in Cuba, Eritrea, and Germany, with 85. 93%,79. 39%. It is also the most popular browser in many other African countries. According to Mozilla, as of December 2014 there were half a billion Firefox users around the world, the Firefox project began as an experimental branch of the Mozilla project by Dave Hyatt, Joe Hewitt, and Blake Ross. They believed the requirements of Netscapes sponsorship and developer-driven feature creep compromised the utility of the Mozilla browser. To combat what they saw as the Mozilla Suites software bloat, they created a stand-alone browser, on April 3,2003, the Mozilla Organization announced that they planned to change their focus from the Mozilla Suite to Firefox and Thunderbird. The community-driven SeaMonkey was formed and eventually replaced the Mozilla Application Suite in 2005, the Firefox project has undergone several name changes. Phoenix was renamed due to issues with Phoenix Technologies, the replacement name, Firebird. In response, the Mozilla Foundation stated that the browser would always bear the name Mozilla Firebird to avoid confusion, after further pressure, on February 9,2004, Mozilla Firebird became Mozilla Firefox. The name Firefox was said to be derived from a nickname of the red panda, for the abbreviation of Firefox, Mozilla prefers Fx or fx, though it is often abbreviated as FF. The Firefox project went through many versions before the version 1.0 was released on November 9,2004, search, which is a front end of Microsoft search engine Bing, by default in most localizations. Firefox Hello is scheduled to be removed in September 2016, functions can be added through add-ons created by third-party developers
32.
Opera (web browser)
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Opera is a web browser for Windows, macOS, and Linux operating systems. It is developed by Opera Software, on 4 November 2016 Operas consumer business, including the browser, was acquired by a Chinese group of investors under the name Golden Brick Capital Private Equity Fund I Limited Partnership. It uses the Blink layout engine, an earlier version using the Presto layout engine is still available, and runs on FreeBSD systems. According to Opera Software, the browser had more than 350 million users worldwide in the 4th quarter of 2014, total Opera mobile users reached 291 million in June 2015. According to SlashGeek, Opera has originated features later adopted by other web browsers, including Speed Dial, pop-up blocking, browser sessions, private browsing, Opera began in 1994 as a research project at Telenor, the largest Norwegian telecommunications company. In 1995, it branched out into a company named Opera Software ASA. Opera was first released publicly in 1996 with version 2.0, in an attempt to capitalize on the emerging market for Internet-connected handheld devices, a project to port Opera to mobile device platforms was started in 1998. Opera 4.0, released in 2000, included a new core that facilitated creation of editions of Opera for multiple operating systems and platforms. Up to this point, Opera was trialware and had to be purchased after the period ended. Version 5.0 saw the end of this requirement, instead, Opera became ad-sponsored, displaying advertisements to users who had not paid for it. Later versions of Opera gave the user the choice of seeing banner ads or targeted text advertisements from Google, with version 8.5 the advertisements were removed entirely and primary financial support for the browser came through revenue from Google. This feature was improved and expanded in version 9.5, when GeoTrust was replaced with Netcraft. Also in 2006, Opera Software ASA released Internet Channel and Nintendo DS Browser for Nintendos DS, a new JavaScript engine called Carakan, after the Javanese alphabet, was introduced with version 10.50. According to Opera Software, Carakan makes Opera 10.50 more than seven times faster in SunSpider than Opera 10.10, on 16 December 2010, Opera 11 was released, featuring extensions, tab stacking, visual mouse gestures, and changes to the address bar. Opera 12 was released on 14 June 2012, on 12 February 2013, Opera Software announced that it would drop its own Presto layout engine in favour of WebKit as implemented by Googles Chrome browser, using code from the Chromium project. Opera Software also planned to contribute code to WebKit, on 28 May 2013, a beta release of Opera 15 was made available, the first version based on the Chromium project. Many distinctive features of the versions were dropped, and Opera Mail was separated into a standalone application derived from Opera 12. In July 2016, the Opera browser was sold to Qihoo for $600 million, on 4 November 2016 Golden Brick Capital completed the acquisition
33.
Google Chrome
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Google Chrome is a freeware web browser developed by Google. It was first released in 2008, for Microsoft Windows, and was ported to Linux, macOS, iOS. Google Chrome is also the component of Chrome OS, where it serves as a platform for running web apps. Google releases the majority of Chromes source code as the Chromium open-source project, a notable component that is not open-source is the built-in Adobe Flash Player. Chrome used the WebKit layout engine until version 27, as of version 28, all Chrome ports except the iOS port use Blink, a fork of the WebKit engine. As of February 2017, StatCounter estimates that Google Chrome has a 62% worldwide usage share of web browsers as a desktop browser and it also has 52% market share across all platforms combined, because it is also the most popular browser for smartphones. Its success has led to Google expanding the Chrome brand name on other products such as Chromecast, Chromebook, Chromebit, Chromebox. Google CEO Eric Schmidt opposed the development of an independent web browser for six years and he stated that at the time, Google was a small company, and he did not want to go through bruising browser wars. Rumors of Google building a web browser first appeared in September 2004, online journals and U. S. newspapers stated at the time that Google was hiring former Microsoft web developers among others. It also came shortly after the final 1.0 release of Mozilla Firefox, the release announcement was originally scheduled for September 3,2008, and a comic by Scott McCloud was to be sent to journalists and bloggers explaining the features within the new browser. Google subsequently made the comic available on Google Books and mentioned it on their blog along with an explanation for the early release. The browser was first publicly released on September 2,2008 for Windows XP and later, with 43 supported languages, officially a beta version and this passage was inherited from the general Google terms of service. Google responded to this criticism immediately by stating that the language used was borrowed from other products, Chrome quickly gained about 1% usage share. After the initial surge, usage share dropped until it hit a low of 0. 69% in October 2008 and it then started rising again and by December 2008, Chrome again passed the 1% threshold. In early January 2009, CNET reported that Google planned to release versions of Chrome for OS X, in December 2009, Google released beta versions of Chrome for OS X and Linux. Google Chrome 5.0, announced on May 25,2010, was the first stable release to all three platforms. Chrome was one of the twelve browsers offered to European Economic Area users of Microsoft Windows in 2010, the V8 JavaScript virtual machine was considered a sufficiently important project to be split off and handled by a separate team in Denmark coordinated by Lars Bak at Aarhus. Chrome initially used the WebKit rendering engine to display web pages, in 2013, they forked the WebCore component to create their own layout engine Blink
34.
Safari (web browser)
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Safari is a web browser developed by Apple based on the WebKit engine. First released in 2003 with Mac OS X Panther, a version has been included in iOS devices since the introduction of the iPhone in 2007. It is the browser on Apple devices. A Windows version, now discontinued, was available from 2007 to 2012, until 1997, Apple Macintosh computers were shipped with the Netscape Navigator and Cyberdog web browsers only. Internet Explorer for Mac was later included as the web browser for Mac OS8.1 and onwards. Microsoft ultimately released a Mac OS X edition of Internet Explorer for Mac, on January 7,2003, at Macworld San Francisco, Steve Jobs announced that Apple had developed their own web browser, called Safari. It was based on Apples internal fork of the KHTML rendering engine, Apple released the first beta version for OS X that day. A number of official and unofficial beta versions followed, until version 1.0 was released on June 23,2003. 1.0.3, released on August 13,2004 was the last version to support Mac OS X v10.2, while 1.3.2, however,10.3 received security updates through 2007. On April 27,2005, he announced that his development version of Safari now passed the test, Safari 2.0 was released on April 29,2005, as the only web browser included with Mac OS X v10.4. This version was touted by Apple as possessing a 1. 8x speed boost over version 1.2.4, Apple eventually released version 2.0.2 of Safari, which included the modifications required to pass Acid2, on October 31,2005. In June 2005, after criticism from KHTML developers over lack of access to change logs, Apple moved the development source code. WebKit itself was released as open source. The source code for non-renderer aspects of the browser, such as its GUI elements, the final stable version of Safari 2, Safari 2.0.4, was released on January 10,2006 for Mac OS X. It was only available as part of Mac OS X Update 10.4.4 and this version addresses layout and CPU usage issues, among others. Safari 2.0.4 was the last version to be released exclusively on Mac OS X until version 6 in 2012, on January 9,2007, at Macworld SF, Jobs announced Apples iPhone, which would use a mobile version of the Safari browser. On June 11,2007, at the Apple Worldwide Developers Conference, Jobs announced Safari 3 for Mac OS X v10.5, Windows XP, and Windows Vista. During the announcement, he ran a benchmark based on the iBench browser test suite comparing the most popular Windows browsers, hence claiming that Safari was the fastest browser
35.
Chemistry Development Kit
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The Chemistry Development Kit is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS and it is free and open-source software distributed under the GNU Lesser General Public License 2.0. The first source code release was made on 11 May 2011, since then more than 75 people have contributed to the project, leading to a rich set of functions, as given below. Between 2004 and 2007, CDK News was the newsletter of which all articles are available from a public archive. Due to a rate of contributions, the newsletter was put on hold. Later, unit testing, code quality checking, and Javadoc validation was introduced, rajarshi Guha developed a nightly build system, named Nightly, which is still operating at Uppsala University. In 2012, the became a support of the InChI Trust. The library uses JNI-InChI to generate International Chemical Identifiers, in April 2013, John Mayfield joined the ranks of release managers of the CDK, to handle the development branch. The CDK is a library, instead of a user program, however, it has been integrated into various environments to make its functions available. CDK is currently used in applications, including the programming language R, CDK-Taverna, Bioclipse, PaDEL. Also, CDK extensions exist for Konstanz Information Miner and for Excel, in 2008, bits of GPL-licensed code were removed from the library. While those code bits were independent from the main CDK library, and no copylefting was involved, to reduce confusions among users, the ChemoJava project was instantiated. org
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