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JSmol
JMOL is computer software for molecular modelling chemical structures in 3-dimensions . Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry . It is written in the programming language Java , so it can run on the operating systems Windows , macOS , Linux , and Unix , if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna . A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways. For example, molecules can be displayed as ball-and-stick models , space-filling models , ribbon diagrams , etc. Jmol supports a wide range of chemical file formats , including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML). There is also a JavaScript -only ( HTML5 ) version, _JSmol_, that can be used on computers with no Java. The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development
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Judgment As A Matter Of Law
JUDGMENT AS A MATTER OF LAW (JMOL) is a motion made by a party, during trial, claiming the opposing party has insufficient evidence to reasonably support its case. JMOL is also known as a directed verdict , which it has replaced in American federal courts. JMOL is similar to judgment on the pleadings and summary judgment , all of which test the factual sufficiency of a claim. Judgment on the pleadings is a motion made after pleading and before discovery ; summary judgment happens after discovery and before trial; JMOL occurs during trial. In United States federal courts , JMOL is a creation of Federal Rules of Civil Procedure Rule 50. JMOL is decided by the standard of whether a reasonable jury could find in favor of the party opposing the JMOL motion. If there is no evidence to support a reasonable conclusion for the opposing party, judgment is entered by the court and the case is over. If there is sufficient evidence to make a reasonable conclusion in favor of the opposing party, but there is equally strong evidence to support an opposite conclusion, the party with the burden of persuasion fails. Timing is very important in making a motion for JMOL; the motion can be made only after the opposing party has presented its case. In civil cases, the plaintiff presents its case, then the defendant presents its case, and then the plaintiff may present a rebuttal
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Streptavidin
STREPTAVIDIN /ˌstrɛpˈtævɪdɪn/ is a 52.8 kDa protein purified from the bacterium _ Streptomyces avidinii _. Streptavidin homo-tetramers have an extraordinarily high affinity for biotin (also known as vitamin B7 or vitamin H). With a dissociation constant (Kd) 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. Streptavidin is used extensively in molecular biology and bionanotechnology due to the streptavidin-biotin complex's resistance to organic solvents, denaturants (e.g. guanidinium chloride ), detergents (e.g. SDS , Triton ), proteolytic enzymes, and extremes of temperature and pH. CONTENTS * 1 Structure * 2 Origins of the high affinity to biotin * 3 Uses in Biotechnology * 4 Variants with a Controlled Number of Biotin Binding Sites * 5 Comparison to avidin * 6 References * 7 Further reading * 8 External links STRUCTURE Tetrameric structure of streptavidin with 2 bound biotins 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 and using multiple isomorphous replacement by Weber et al. at E. I. DuPont Central Research and Development Department
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Software Developer
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 often used with similar meanings are programmer , software analyst , and software engineer . According to developer Eric Sink, the differences between system design, software development , and programming are more apparent. Already in the current market place there can be found a segregation between programmers and developers, being that one who implements is not the same as the one who designs the class structure or hierarchy. Even more so that developers become systems architects , those who design the multi-leveled architecture or component interactions of a large software system. (see also Debate over who is a software engineer ) In a large company, there may be employees whose sole responsibility consists of only one of the phases above. In smaller development environments, a few people or even a single individual might handle the complete process. CONTENTS* 1 History * 1.1 Qualifications and Skills * 2 See also * 3 References * 4 External links HISTORYThe word "software" was coined as a prank as early as 1953, but did not appear in print until the 1960's. Before this time, computers were programmed either by customers, or the few commercial computer vendors of the time, such as UNIVAC
UNIVAC
and IBM
IBM

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Software Release Life Cycle
A SOFTWARE RELEASE LIFE CYCLE is the sum of the stages of development and maturity for a piece of computer software : ranging from its initial development to its eventual release, and including updated versions of the released version to help improve software or fix software bugs still present in the software. CONTENTS * 1 History * 2 Stages of development * 2.1 Pre-alpha * 2.2 Alpha * 2.3 Beta * 2.3.1 Open and closed beta * 2.4 Release candidate * 3 Release * 3.1 Release to manufacturing (RTM) * 3.2 General availability (GA) * 3.3 Release to web (RTW) * 4 Support * 4.1 End-of-life * 5 See also * 6 References * 7 Bibliography HISTORYUsage of the "alpha/beta" test terminology originated at IBM
IBM
. As long ago as the 1950s (and probably earlier), IBM
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. As software became a significant part of IBM's offerings, the alpha test terminology was used to denote the pre-announcement test and beta test was used to show product readiness for general availability. Martin Belsky, a manager on some of IBM's earlier software projects claimed to have invented the terminology
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Repository (version Control)
In revision control systems , a REPOSITORY is an on-disk data structure which stores metadata for a set of files and/or directory structure. Depending on whether the version control system in use is distributed (for instance, Git or Mercurial ) or centralized (Subversion or Perforce , for example), the whole set of information in the repository may be duplicated on every user's system or may be maintained on a single server . Some of the metadata that a repository contains includes, among other things: * A historical record of changes in the repository. * A set of commit objects. * A set of references to commit objects, called _heads_.STORING CHANGESThe main purpose of a repository is to store a set of files, as well as the history of changes made to those files. Exactly how each revision control system handles storing those changes, however, differs greatly: for instance, Subversion has in the past relied on a database instance and has since moved to storing its changes directly on the filesystem. These differences in methodology have generally led to diverse uses of revision control by different groups, depending on their needs. SEE ALSO * Software repository * Codebase * Forge (software) * Comparison of source code hosting facilities REFERENCES * ^ "SVNBook". Retrieved 2012-04-20. * ^ "Getting Started - About Version Control". Git SCM
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Java (programming Language)
JAVA is a general-purpose computer programming language that is concurrent , class-based , object-oriented , and specifically designed to have as few implementation dependencies as possible. It is intended to let application developers "write once, run anywhere " (WORA), meaning that compiled Java code can run on all platforms that support Java without the need for recompilation. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of computer architecture . As of 2016, Java is one of the most popular programming languages in use , particularly for client-server web applications, with a reported 9 million developers. Java was originally developed by James Gosling at Sun Microsystems (which has since been acquired by Oracle Corporation ) and released in 1995 as a core component of Sun Microsystems' Java platform . The language derives much of its syntax from C and C++
C++
, but it has fewer low-level facilities than either of them. The original and reference implementation Java compilers , virtual machines, and class libraries were originally released by Sun under proprietary licenses. As of May 2007, in compliance with the specifications of the Java Community Process , Sun relicensed most of its Java technologies under the GNU General Public License
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Operating System
An OPERATING SYSTEM (OS) is system software that manages computer hardware and software resources and provides common services for computer programs . All computer programs , excluding firmware , require an operating system to function. Time-sharing operating systems schedule tasks for efficient use of the system and may also include accounting software for cost allocation of processor time , mass storage , printing , and other resources. For hardware functions such as input and output and memory allocation , the operating system acts as an intermediary between programs and the computer hardware, although the application code is usually executed directly by the hardware and frequently makes system calls to an OS function or is interrupted by it. Operating systems are found on many devices that contain a computer – from cellular phones and video game consoles to web servers and supercomputers . The dominant desktop operating system is Microsoft Windows with a market share of around 83.3%. macOS by Apple Inc. is in second place (11.2%), and the varieties of Linux
Linux
is in third position (1.55%)
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Cross-platform
In computing , CROSS-PLATFORM SOFTWARE (also MULTI-PLATFORM SOFTWARE or PLATFORM-INDEPENDENT SOFTWARE) is computer software that is implemented on multiple computing platforms . Cross-platform software may be divided into two types; one requires individual building or compilation for each platform that it supports, and the other one can be directly run on any platform without special preparation, e.g., software written in an interpreted language or pre-compiled portable bytecode for which the interpreters or run-time packages are common or standard components of all platforms. For example, a cross-platform application may run on Microsoft Windows on the x86 architecture , Linux
Linux
on the x86 architecture and macOS on either the PowerPC or x86-based Apple Macintosh
Macintosh
systems. Cross-platform programs may run on as many as all existing platforms, or on as few as two platforms. Cross-platform frameworks (such as Qt , Xamarin , Phonegap , or Ionic ) exist to aid cross-platform development
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Computing Platform
A COMPUTING PLATFORM is the environment in which a piece of software is executed. It may be the hardware or the operating system (OS), even a web browser or other underlying software, as long as the program code is executed in it. Computing platforms have different abstraction levels, including a computer architecture , an OS, or runtime libraries . A computing platform is the stage on which computer programs can run. A platform can be seen both as a constraint on the software development process , in that different platforms provide different functionality and restrictions; and as an assistance to the development process, in that they provide low-level functionality ready-made. For example, an OS may be a platform that abstracts the underlying differences in hardware and provides a generic command for saving files or accessing the network . CONTENTS * 1 Components * 2 Operating system examples * 2.1 Desktop, laptop, server * 2.2 Mobile * 3 Software frameworks * 4 Hardware examples * 5 See also * 6 References * 7 External links COMPONENTSPlatforms 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 hardware+OS platform, but this is not relevant to software running within the browser
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Java (software Platform)
JAVA is a set of computer software and specifications developed by Sun Microsystems , which was later acquired by the Oracle Corporation , that provides a system for developing application software and deploying it in a cross-platform computing environment. 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 and can be embedded in HTML pages. Writing in the Java programming language is the primary way to produce code that will be deployed as byte code in a Java Virtual Machine (JVM); byte code compilers are also available for other languages, including Ada , JavaScript , Python , and Ruby . 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 and Objective-C . 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
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Web Browser
A WEB BROWSER (commonly referred to as a 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 (URI/URL) that may be a web page , image, video or other piece of content. 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, they can also be used to access information provided by web servers in private networks or files in file systems . The most popular web browsers are Chrome , Edge (preceded by Internet Explorer ), Safari , Opera and Firefox . CONTENTS * 1 History * 2 Business models * 3 Function * 4 Market share * 5 Features * 5.1 User interface * 5.2 Privacy and security * 5.3 Standards support * 5.4 Extensibility * 6 Components * 7 See also * 8 References * 9 External links HISTORY Main article: History of the web browser The first web browser was invented in 1990 by Sir Tim Berners-Lee . Berners-Lee is the director of the World Wide Web Consortium (W3C), which oversees the Web's continued development, and is also the founder of the World Wide Web Foundation. His browser was called WorldWideWeb and later renamed Nexus
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Molecular Modelling
MOLECULAR MODELLING encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules . The methods are used in the fields of computational chemistry , drug design , computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. 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 (a molecular mechanics approach), or explicitly modelling electrons of each atom (a quantum chemistry approach). CONTENTS * 1 Molecular mechanics * 2 Variables * 2.1 Coordinate representations * 3 Applications * 4 See also * 5 Notes * 6 External links MOLECULAR MECHANICS Molecular mechanics is one aspect of molecular modelling, as it refers to the use of classical mechanics ( Newtonian mechanics ) to describe the physical basis behind the models. Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. The interactions between neighbouring atoms are described by spring-like interactions (representing chemical bonds ) and Van der Waals forces
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Software License
A SOFTWARE LICENSE is a legal instrument (usually by way of contract law , with or without printed material) governing the use or redistribution of software. Under United States copyright law all software is copyright protected, in source code as also object code form. The only exception is software in the public domain . A typical software license grants the licensee , typically an end-user , permission to use one or more copies of software in ways where such a use would otherwise potentially constitute copyright infringement of the software owner's exclusive rights under copyright law. CONTENTS* 1 Software
Software
licenses and copyright law * 1.1 Ownership vs. licensing * 2 Proprietary software licenses * 3 Free and open-source software licenses * 4 See also * 5 References * 6 External links SOFTWARE LICENSES AND COPYRIGHT LAWMost distributed software can be categorized according to its license type (see table). Two common categories for software under copyright law, and therefore with licenses which grant the licensee specific rights, are proprietary software and free and open source software (FOSS)
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GNU Lesser General Public License
The GNU
GNU
LESSER GENERAL PUBLIC LICENSE (LGPL) is a free software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate software released under the LGPL into their own (even proprietary ) software without being required by the terms of a strong copyleft license to release the source code of their own components. The license only requires software under the LGPL be modifiable by end users via source code availability. For proprietary software, code under the LGPL is usually used in the form of a shared library , so that there is a clear separation between the proprietary and LGPL components. The LGPL is primarily used for software libraries , although it is also used by some stand-alone applications. The LGPL was developed as a compromise between the strong copyleft of the GNU General Public License (GPL) and more permissive licenses such as the BSD licenses and the MIT License . The word "Lesser" in the title shows that the LGPL does not guarantee the end user's complete freedom in the use of software; it only guarantees the freedom of modification for components licensed under the LGPL, but not for any proprietary components
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Software
COMPUTER SOFTWARE, or simply SOFTWARE, is a 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 and data. 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 realistically 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 (CPU). 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 particular storage location in the computer—an effect that is not directly observable to the user. An instruction may also (indirectly) cause something to appear on a display of the computer system—a state change which should be visible to the user
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