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JSmol
JMOL is computer software for molecular modelling chemical structures in 3-dimensions . Jmol
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
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
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HTML5
HTML5
HTML5
is a markup language used for structuring and presenting content on the World Wide Web
World Wide Web
. It is the fifth and current major version of the HTML
HTML
standard. It was published in October 2014 by the World Wide Web
World Wide Web
Consortium (W3C) to improve the language with support for the latest multimedia, while keeping it both easily readable by humans and consistently understood by computers and devices such as web browsers , parsers , etc. HTML5
HTML5
is intended to subsume not only HTML
HTML
4 , but also X HTML
HTML
1 and DOM Level 2 HTML
HTML

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JavaScript
com.netscape.javascript-source TYPE OF FORMAT Scripting language Part of a series on JAVASCRIPT * JavaScript syntax * JavaScript library * Unobtrusive JavaScript * JavaScript engine LISTS OF FRAMEWORKS AND LIBRARIES * Ajax frameworks * JavaScript
JavaScript
web frameworks * Comparison of JavaScript frameworks * List of JavaScript libraries * JavaScript
JavaScript
unit testing frameworks JAVASCRIPT OBJECT NOTATION See also * ECMAScript * v * t * e JAVASCRIPT (/ˈdʒɑːvəˌskrɪpt/ ), often abbreviated as JS, is a high-level , dynamic , weakly typed , object-based , multi-paradigm , and interpreted programming language
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MDL Chime
MDL CHIME is a free plugin used by web browsers to display the three-dimensional structures of molecules . It is part of the ISIS product line acquired by Symyx Technologies from scientific publisher Elsevier
Elsevier
in October 2007. It is based on the RasMol code. Chime is used by a wide range of biochemistry web sites for the visualization of macromolecules . Many of these sites are linked to the World Index of Molecular Visualization Resources MolVisIndex.Org. Chime was also used until 2006 at the Protein Data Bank to examine structures stored there
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Plug-in (computing)
In computing , a PLUG-IN (or PLUGIN, ADD-IN, ADDIN, ADD-ON, ADDON, or EXTENSION) 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. Well-known browser plug-ins include the Adobe Flash Player , the QuickTime Player , and the Java plug-in, which can launch a user-activated Java applet
Java applet
on a web page to its execution on a local Java virtual machine
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Internet Explorer
INTERNET EXPLORER (formerly MICROSOFT INTERNET EXPLORER and WINDOWS INTERNET EXPLORER, commonly abbreviated IE or MSIE) is a series of graphical web browsers developed by Microsoft
Microsoft
and included in the Microsoft
Microsoft
Windows
Windows
line of operating systems , starting in 1995. It was first released as part of the add-on package Plus! for Windows
Windows
95 that year. Later versions were available as free downloads, or in service packs , and included in the original equipment manufacturer (OEM) service releases of Windows
Windows
95 and later versions of Windows. The browser is discontinued , but still maintained . Internet
Internet
Explorer was one of the most widely used web browsers, attaining a peak of about 95% usage share during 2002 and 2003
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Chemical Markup Language
CHEMICAL MARKUP LANGUAGE (CHEMML or CML) is an approach to managing molecular information using tools such as XML
XML
and Java . It was the first domain specific implementation based strictly on XML
XML
, first based on a DTD and later on an XML
XML
Schema , the most robust and widely used system for precise information management in many areas. It has been developed over more than a decade by Murray-Rust , Rzepa and others and has been tested in many areas and on a variety of machines. Chemical information is traditionally stored in many different file types which inhibit reuse of the documents. CML uses XML's portability to help CML developers and chemists design interoperable documents. There are a number of tools that can generate, process and view CML documents. Publishers can distribute chemistry within XML
XML
documents by using CML, e.g. in RSS documents
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Ribbon Diagram
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. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the image at the right. 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 polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon. Ribbon diagrams are simple, yet powerful, in expressing the visual basics of a molecular structure (twist, fold and unfold)
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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
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
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Apache Taverna
APACHE TAVERNA is an open source software tool for designing and executing workflows , initially created by the myGrid project under the name Taverna Workbench, now a project under the Apache incubator . Taverna allows users to integrate many different software components, including WSDL SOAP
SOAP
or REST Web services , such as those provided by the National Center for Biotechnology Information , the European Bioinformatics Institute , the DNA Databank of Japan (DDBJ) , SoapLab , BioMOBY and EMBOSS . 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
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Ball-and-stick Model
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. In a good model, the angles between the rods should be the same as the angles between the bonds , and the distances between the centers of the spheres should be proportional to the distances between the corresponding atomic nuclei . The chemical element of each atom is often indicated by the sphere's 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 a clear insight about the space occupied by the model
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Space-filling Model
In chemistry , a SPACE-FILLING MODEL, also known as a calotte model, is a type of three-dimensional (3D) molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic nuclei , all in the same scale. Atoms of different chemical elements are usually represented by spheres of different colors. Space-filling calotte models are also referred to as CPK MODELS after the chemists Robert Corey , Linus Pauling , and Walter Koltun , who over a span of time developed the modeling concept into a useful form. They are distinguished from other 3D representations, such as the ball-and-stick and skeletal models, by the use of the "full size" space-filling spheres for the atoms
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Mozilla Firefox 2
MOZILLA FIREFOX 2 is a version of Firefox
Firefox
, a web browser released on October 24, 2006 by the Mozilla Corporation . Firefox
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
Firefox
1.5, including improved support for Scalable Vector Graphics (SVG) and JavaScript
JavaScript
1.7, as well as user interface changes. On March 22, 2006, the first alpha version of Firefox
Firefox
2 (Bon Echo Alpha 1) was released. It featured Gecko 1.8.1 for the first time. Mozilla
Mozilla
Firefox
Firefox
2.0.0.x is the final version officially supported on Windows NT 4.0 and Windows 98, although it can run on Windows 95 using tweaks
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Netscape Communicator
NETSCAPE COMMUNICATOR (or Netscape
Netscape
4) is a discontinued Internet suite produced by Netscape Communications Corporation , and was the fourth major release in the Netscape
Netscape
line of browsers. It was first in beta in 1996 and was released in June 1997. Netscape
Netscape
Communicator addressed the problem of Netscape Navigator
Netscape Navigator
3.x being used as both the name of the suite and the browser contained within it by renaming the suite to Netscape
Netscape
Communicator. It included more groupware features intended to appeal to enterprises
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Comparison Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for MOLECULAR MECHANICS calculations
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Molecule Editor
A MOLECULE EDITOR is a computer program for creating and modifying representations of chemical structures . Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space , via 2D computer graphics
2D computer graphics
or 3D computer graphics
3D computer graphics
, respectively. Two-dimensional output is used as illustrations or to query chemical databases . Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages. Database molecular editors such as Leatherface, RECAP, and Molecule Slicer allow large numbers of molecules to be modified automatically according to rules such as 'deprotonate carboxylic acids' or 'break exocyclic bonds' that can be specified by a user. Molecule editors typically support reading and writing at least one file format or line notation
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