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
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