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Chemistry Development Kit
The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0. History The CDK was created by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, then developers of Jmol and JChemPaint, to provide a common code base, on 27–29 September 2000 at the University of Notre Dame. The first source code release was made on 11 May 2011. Since then more than 100 people have contributed to the project, leading to a rich set of functions, as given below. Between 2004 and 2007, ''CDK News'' was the project's newsletter of which all articles are available from a public archive. Due to an unsteady rate of contributions, the newsletter was put on hold. Later, unit testing, code quality checking, and Javadoc validation was introduced. Rajarshi Guha developed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Christoph Steinbeck
Christoph Steinbeck (born 1966 in Neuwied) is a German chemist and has a professorship for analytical chemistry, cheminformatics and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia, Germany. Education Steinbeck received his PhD from the University of Bonn in 1995 for work on LUCY, a software program for structural elucidation from nuclear magnetic resonance (NMR) correlation experiments. In 2003 he received his habilitation. Research Steinbeck's research interests have involved the elucidation of chemical structures of metabolites. He was one of the first chemists to develop open source tools for cheminformatics. He initiated JChemPaint, was founder of the Chemistry Development Kit, and is responsible for leading the team working on Chemical Entities of Biological Interest (ChEBI). He headed the Cheminformatics and Metabolomics group at the European Molecular Biology Laboratory-European Bioinformatics Institute in Cambridge, United Kingdom from 2008 to 201 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jmol
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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 or 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. Examples of each include Molfile and simplified molecular input line entry specification (SMILES), respectively. Files generated by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microsoft Excel
Microsoft Excel is a spreadsheet developed by Microsoft for Microsoft Windows, Windows, macOS, Android (operating system), Android and iOS. It features calculation or computation capabilities, graphing tools, pivot tables, and a macro (computer science), macro programming language called Visual Basic for Applications (VBA). Excel forms part of the Microsoft Office suite of software. Features Basic operation Microsoft Excel has the basic features of all spreadsheets, using a grid of ''cells'' arranged in numbered ''rows'' and letter-named ''columns'' to organize data manipulations like arithmetic operations. It has a battery of supplied functions to answer statistical, engineering, and financial needs. In addition, it can display data as line graphs, histograms and charts, and with a very limited three-dimensional graphical display. It allows sectioning of data to view its dependencies on various factors for different perspectives (using ''pivot tables'' and the ''sce ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
KNIME
KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept. A graphical user interface and use of JDBC allows assembly of nodes blending different data sources, including preprocessing ( ETL: Extraction, Transformation, Loading), for modeling, data analysis and visualization without, or with only minimal, programming. Since 2006, KNIME has been used in pharmaceutical research, it also used in other areas such as CRM customer data analysis, business intelligence, text mining and financial data analysis. Recently attempts were made to use KNIME as robotic process automation (RPA) tool. KNIME's headquarters are based in Zurich, with additional offices in Konstanz, Berlin, and Austin (USA). History The Development of KNIME was started January 2004 by a team of software enginee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioclipse
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009, and a command line version in 2021. Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality. The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, and OpenTox were added. Bioclipse is developed as a collaboration between the Prot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Taverna Workbench
Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name ''Taverna Workbench'', then a project under the Apache incubator. Taverna allowed users to integrate many different software components, including WSDL 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 was not finite and users could import new service descriptions into the Taverna Workbench. Taverna Workbench provided a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow engine was also available separately, as a Java API, command line tool or as a server. Taverna was used by users in many domains, such as bioinformatics, cheminformatics, medicine, astronomy, social science, music, and digital preservation. Som ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
International Chemical Identifier
The International Chemical Identifier (InChI or ) is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web. Initially developed by the International Union of Pure and Applied Chemistry (IUPAC) and National Institute of Standards and Technology (NIST) from 2000 to 2005, the format and algorithms are non-proprietary. Since May 2009, it has been developed by the InChI Trust, a nonprofit charity from the United Kingdom which works to implement and promote the use of InChI. The identifiers describe chemical substances in terms of ''layers'' of information — the atoms and their bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information. Not all layers have to be provided; for instance, the tautomer layer can be omitted if that type of information is not relevant to the particular appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
InChI Trust
The International Chemical Identifier (InChI or ) is a textual identifier for chemical substance A chemical substance is a form of matter having constant chemical composition and characteristic properties. Some references add that chemical substance cannot be separated into its constituent elements by physical separation methods, i.e., wi ...s, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web. Initially developed by the International Union of Pure and Applied Chemistry (IUPAC) and National Institute of Standards and Technology (NIST) from 2000 to 2005, the format and algorithms are non-proprietary. Since May 2009, it has been developed by the InChI Trust, a nonprofit charity from the United Kingdom which works to implement and promote the use of InChI. The identifiers describe chemical substances in terms of ''layers'' of information — the atoms and their bond connectivi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Uppsala University
Uppsala University ( sv, Uppsala universitet) is a public university, public research university in Uppsala, Sweden. Founded in 1477, it is the List of universities in Sweden, oldest university in Sweden and the Nordic countries still in operation. The university rose to significance during the rise of Swedish Empire, Sweden as a great power at the end of the 16th century and was then given a relative financial stability with a large donation from King Gustavus Adolphus of Sweden, Gustavus Adolphus in the early 17th century. Uppsala also has an important historical place in Swedish national culture, identity and for the Swedish establishment: in historiography, literature, politics, and music. Many aspects of Swedish academic culture in general, such as the white student cap, originated in Uppsala. It shares some peculiarities, such as the student nation system, with Lund University and the University of Helsinki. Uppsala belongs to the Coimbra Group of European universities a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Javadoc
Javadoc (originally cased JavaDoc) is a documentation generator created by Sun Microsystems for the Java language (now owned by Oracle Corporation) for generating API documentation in HTML format from Java source code. The HTML format is used for adding the convenience of being able to hyperlink related documents together. The "doc comments" format used by Javadoc is the de facto industry standard for documenting Java classes. Some IDEs, like IntelliJ IDEA, NetBeans and Eclipse, automatically generate Javadoc templates. Many file editors assist the user in producing Javadoc source and use the Javadoc info as internal references for the programmer. Javadoc also provides an API for creating doclets and taglets, which allows users to analyze the structure of a Java application. This is how JDiff can generate reports of what changed between two versions of an API. Javadoc does not affect performance in Java as all comments are removed at compilation time. Writing comments and Javado ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
