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Metascape
Metascape is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists. Metascape provides automated meta-analysis tools to understand either common or unique pathways and protein networks within a group of orthogonal target-discovery studies. History In the "OMICs" age, it is important to gain biological insights into a list of genes. Although a number of bioinformatics sources exist for this purpose, such as DAVID, they are not all free, easy to use, and well maintained. To analyze multiple lists of genes originated from orthogonal but complementary "OMICs" studies, tools often require computational skills that are beyond the reach of many biologists. According to the Metascape blog, a team of scientists self-organized to address this challenge. The team includes core members Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Christopher Benner, and Sumit Chanda, as well aother contributorsover the time. Metascape was first re ... [...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 (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
The list of bioinformatics software tools can be split up according to the license used: *List of proprietary bioinformatics software *List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software **List of sequence alignment software ** List of alignment visualization software **Alignment-free sequence analysis **De novo sequence assemblers **List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools **List of phylogenetics software **List of phylogenetic tree visualization software ** :Metagenomics_software *Structural biology software **List of molecular graphics systems **List of protein-ligand docking software **List of RNA structure prediction software **List of software for protein model error verification **List of protein secondary structure prediction programs **List of protein struct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Databases
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Docker (software)
Docker is a set of platform as a service (PaaS) products that use OS-level virtualization to deliver software in packages called ''containers''. The service has both free and premium tiers. The software that hosts the containers is called Docker Engine. It was first started in 2013 and is developed by Docker, Inc. Background Containers are isolated from one another and bundle their own software, libraries and configuration files; they can communicate with each other through well-defined channels. Because all of the containers share the services of a single operating system kernel, they use fewer resources than virtual machines. Operation Docker can package an application and its dependencies in a virtual container that can run on any Linux, Windows, or macOS computer. This enables the application to run in a variety of locations, such as on-premises, in public (see decentralized computing, distributed computing, and cloud computing) or private cloud. When running on Linux, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cytoscape
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged. Cytoscape also has a JavaScript-centric sister project nameCytoscape.jsthat can be used to analyse and visualise graphs in JavaScript environments, like a browser. History Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002, and v1.0 w ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microsoft PowerPoint
Microsoft PowerPoint is a presentation program, created by Robert Gaskins and Dennis Austin at a software company named Forethought, Inc. It was released on April 20, 1987, initially for Macintosh computers only. Microsoft acquired PowerPoint for about $14 million three months after it appeared. This was Microsoft's first significant acquisition, and Microsoft set up a new business unit for PowerPoint in Silicon Valley where Forethought had been located. PowerPoint became a component of the Microsoft Office suite, first offered in 1989 for Macintosh and in 1990 for Windows, which bundled several Microsoft apps. Beginning with PowerPoint 4.0 (1994), PowerPoint was integrated into Microsoft Office development, and adopted shared common components and a converged user interface. PowerPoint's market share was very small at first, prior to introducing a version for Microsoft Windows, but grew rapidly with the growth of Windows and of Office. Since the late 1990s, PowerPoint ... [...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] |
STRING
String or strings may refer to: *String (structure), a long flexible structure made from threads twisted together, which is used to tie, bind, or hang other objects Arts, entertainment, and media Films * ''Strings'' (1991 film), a Canadian animated short * ''Strings'' (2004 film), a film directed by Anders Rønnow Klarlund * ''Strings'' (2011 film), an American dramatic thriller film * ''Strings'' (2012 film), a British film by Rob Savage * ''Bravetown'' (2015 film), an American drama film originally titled ''Strings'' * ''The String'' (2009), a French film Music Instruments * String (music), the flexible element that produces vibrations and sound in string instruments * String instrument, a musical instrument that produces sound through vibrating strings ** List of string instruments * String piano, a pianistic extended technique in which sound is produced by direct manipulation of the strings, rather than striking the piano's keys Types of groups * String band, musical ens ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WikiPathways
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is built using MediaWiki software, a custom graphical pathway editing tool ( PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems. Pathway content Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and the supported species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, rice and arabidopsis, as well as bacteria and plant species. Using a search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reactome
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is authored by biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format. The website can be used to browse pathways and submit data to a suite of data analysis tools. The underlying data is fully downloadable in a number of standard formats including PDF, SBML and BioPAX. Pathway diagrams use a Systems Biology Graphical Notation (SBGN)-based style. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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