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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] |
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 deve ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioJava
BioJava is an open-source software project dedicated to provide Java tools to process biological data.VS Matha and P Kangueane, 2009, ''Bioinformatics: a concept-based introduction'', 2009. p26 BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid applicat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MyExperiment
myExperiment is a social web site for researchers sharing research objects such as scientific workflows. The myExperiment website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as Bioclipse. myExperiment has a REST API and is based on an open source Ruby on Rails codebase. It supports Linked data and has a SPARQL Endpoint, with ainteractive tutorial The myExperiment project is directed by David De Roure at University of Oxford and is one of the activities of the myGrid consortium led by Carole Goble of The University of Manchester, UK and of the-Research SouthUK regional consortium led by thOxford e-Research Centre It was originally funded by Jisc under the Virtual Research Environment programme and by the Microsoftbr>Technical Computing Initiative myExperiment is being enhanced by the workflows for ever project (Wf4Ever) which aims to provide new fea ... [...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 ( ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms ( SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties ... [...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 2 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Bioinformatics Software
Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procure political rights, as for a disenfranchised group * Free will, control exercised by rational agents over their actions and decisions * Free of charge, also known as gratis. See Gratis vs libre. Computing * Free (programming), a function that releases dynamically allocated memory for reuse * Free format, a file format which can be used without restrictions * Free software, software usable and distributable with few restrictions and no payment * Freeware, a broader class of software available at no cost Mathematics * Free object ** Free abelian group ** Free algebra ** Free group ** Free module ** Free semigroup * Free variable People * Free (surname) * Free (rapper) (born 1968), or Free Marie, American rapper and media pers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Groovy (programming Language)
Apache Groovy is a Java-syntax-compatible object-oriented programming language for the Java platform. It is both a static and dynamic language with features similar to those of Python, Ruby, and Smalltalk. It can be used as both a programming language and a scripting language for the Java Platform, is compiled to Java virtual machine (JVM) bytecode, and interoperates seamlessly with other Java code and libraries. Groovy uses a curly-bracket syntax similar to Java's. Groovy supports closures, multiline strings, and expressions embedded in strings. Much of Groovy's power lies in its AST transformations, triggered through annotations. Groovy 1.0 was released on January 2, 2007, and Groovy 2.0 in July, 2012. Since version 2, Groovy can be compiled statically, offering type inference and performance near that of Java. Groovy 2.4 was the last major release under Pivotal Software's sponsorship which ended in March 2015. Groovy has since changed its governance structure to a Proj ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JavaScript
JavaScript (), often abbreviated as JS, is a programming language that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of websites use JavaScript on the client side for webpage behavior, often incorporating third-party libraries. All major web browsers have a dedicated JavaScript engine to execute the code on users' devices. JavaScript is a high-level, often just-in-time compiled language that conforms to the ECMAScript standard. It has dynamic typing, prototype-based object-orientation, and first-class functions. It is multi-paradigm, supporting event-driven, functional, and imperative programming styles. It has application programming interfaces (APIs) for working with text, dates, regular expressions, standard data structures, and the Document Object Model (DOM). The ECMAScript standard does not include any input/output (I/O), such as networking, storage, or graphics facilities. In practice, the web bro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maastricht University
Maastricht University (abbreviated as UM; nl, Universiteit Maastricht) is a public research university in Maastricht, Netherlands. Founded in 1976, it is the second youngest of the thirteen Dutch universities. In 2021, 22,383 students studied at Maastricht University, 56% of whom were foreign students, with over 4,000 employees. About half of the bachelor's programmes are fully offered in English, while the other half is taught wholly or partly in Dutch. Most of the master's and doctoral programmes are in English. Besides traditional programmes, Maastricht University also has three honours liberal arts colleges: University College Maastricht and the Maastricht Science Programme in the same liberal arts tradition. The satellite University College Venlo opened in 2015. Maastricht University regularly ranks as one of Europe's leading universities. The university has been placed in the top 300 universities in the world by five major ranking tables. Maastricht University was at 88th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Karolinska Institutet
The Karolinska Institute (KI; sv, Karolinska Institutet; sometimes known as the (Royal) Caroline Institute in English) is a research-led medical university in Solna within the Stockholm urban area of Sweden. The Karolinska Institute is consistently ranked amongst the world's best medical schools, ranking 6th worldwide for medicine in 2021. The Nobel Assembly at the Karolinska Institute awards the Nobel Prize in Physiology or Medicine. The assembly consists of fifty professors from various medical disciplines at the university. The current rector of Karolinska Institute is Ole Petter Ottersen, who took office in August 2017. The Karolinska Institute was founded in 1810 on the island of Kungsholmen on the west side of Stockholm; the main campus was relocated decades later to Solna, just outside Stockholm. A second campus was established more recently in Flemingsberg, Huddinge, south of Stockholm. The Karolinska Institute is Sweden's third oldest medical school, after Uppsa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Leiden University
Leiden University (abbreviated as ''LEI''; nl, Universiteit Leiden) is a public research university in Leiden, Netherlands. The university was founded as a Protestant university in 1575 by William, Prince of Orange, as a reward to the city of Leiden for its defence against Spanish attacks during the Eighty Years' War. As the oldest institution of higher education in the Netherlands, it enjoys a reputation across Europe and the world. Known for its historic foundations and emphasis on the social sciences, the university came into particular prominence during the Dutch Golden Age, when scholars from around Europe were attracted to the Dutch Republic due to its climate of intellectual tolerance and Leiden's international reputation. During this time, Leiden became the home to individuals such as René Descartes, Rembrandt, Christiaan Huygens, Hugo Grotius, Baruch Spinoza and Baron d'Holbach. The university has seven academic faculties and over fifty subject departments wh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
