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Geworkbench
geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java (programming language), Java. geWorkbench uses a component architecture. , there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (National Institutes of Health Common Fund, NIH Common Fund). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins. Features * Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure predict ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomespace
GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data between tools via automatic format conversion. Analyses can use data from local or cloud-based stores. GenomeSpace consists of a web-based user interface (UI) for users, and both a representational state transfer (RESTful) application programming interface (API) and a Java (programming language), Java-based client development kit (CDK) for developers integrating their applications with GenomeSpace. GenomeSpace tools GenomeSpace is linked with several tools and data sources for genomics analysis: Cytoscape, Galaxy (computational biology), Galaxy, GenePattern, Genomica, Geworkbench, geWorkbench, InSilico DB, the Integrative Genomics Viewer (IGV), and the http://hgwdev-gs.cse.ucsc.edu/cgi-bin/hgTables UCSC Genome Browser. These programs provide a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Open-source Bioinformatics Software
This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia. See also * List of sequence alignment software * List of open-source healthcare software * List of biomedical cybernetics software * List of freeware health software * List of genetic engineering software * List of molecular graphics systems * List of systems biology modelling software * Comparison of software for molecular mechanics modeling * List of proprietary bioinformatics software References External links Free Biology Software– Free Software Directory – Free Software Foundation {{DEFAULTSORT:Open source bioinformatics software Lists of bioinformatics software * Bioinformatics Open Open or OPEN may refer to: Music * Open (band), Australian pop/rock band * The Open (band), English indie rock band * ''Open'' (Blues Image album), 1969 * ''Open'' (Gotthard album), 1999 * ''Open'' (Cowboy Junkies album), 2001 * ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systems Biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionist, reductionism) to biological research. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent property, emergent properties, properties of cell (biology), cells, tissue (biology), tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cluster Analysis
Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters). It is a main task of exploratory data analysis, and a common technique for statistics, statistical data analysis, used in many fields, including pattern recognition, image analysis, information retrieval, bioinformatics, data compression, computer graphics and machine learning. Cluster analysis itself is not one specific algorithm, but the general task to be solved. It can be achieved by various algorithms that differ significantly in their understanding of what constitutes a cluster and how to efficiently find them. Popular notions of clusters include groups with small Distance function, distances between cluster members, dense areas of the data space, intervals or particular statistical distributions. Clustering can therefore be formulated as a multi-object ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software Using The BSD License
Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists of machine language instructions supported by an individual processor—typically a central processing unit (CPU) or a graphics processing unit (GPU). 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 invoke one of many input or output operations, for example displaying some text on a computer screen; causing state changes which should be visible to the user. The processor executes the instructions in the order they are provided, unless it is instructed to ... [...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] |
Genome Compiler
Twist Bioscience is a public biotechnology company based in South San Francisco that manufactures synthetic DNA and DNA products for customers in a wide range of industries. Twist was founded in 2013 by Emily Leproust, Bill Banyai, and Bill Peck. The company was represented by Leproust at a March 2021 tabletop exercise at the Munich Security Conference simulating an outbreak of weaponized monkeypox Monkeypox (also called mpox by the WHO) is an infectious viral disease that can occur in humans and some other animals. Symptoms include fever, swollen lymph nodes, and a rash that forms blisters and then crusts over. The time from exposure t .... References {{Reflist Companies based in South San Francisco, California American companies established in 2013 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genepattern
GenePattern is a freely available computational biology open-source software package originally created and developed at the Broad Institute for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. GenePattern is currently developed at the University of California, San Diego. Functionality GenePattern is a powerful scientific workflow system that provides access to hundreds of genomic analysis tools. Use these analysis tools as building blocks to design sophisticated analysis pipelines that capture the methods, parameters, and data used to produce analysis results. Pipelines can be used to create, edit and share reproducible in silico results. Project Objectives # Accessibility: Run over 200 regularly updated analysis and visualization tools (that support data preprocessing, gene expression analysis, proteomics, Single nucleotide polymorphism (SNP) analysis, flow cy ... [...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] |
National Institutes Of Health Common Fund
The National Institutes of Health Common Fund is an initiative of the National Institutes of Health (NIH) aimed at supporting research collaboration between two or more NIH institutes and centers (ICs). The fund offers flexible support for cutting edge, multidisciplinary, multi-investigator and higher risk research. It is intended to streamline US biomedical research and make it more flexible in response to society's health needs. The high-impact programs it supports are known collectively as the "NIH Roadmap for Medical Research". It is coordinated by the Office of Strategic Coordination, one of the six offices of the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI) within the Office of the Director. Common Fund programs are expected to transform the way a broad spectrum of health research is conducted. Initiatives that comprise Common Fund programs are intended to be catalytic in nature by providing limited term investments in strategic areas to sti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Centers For Biomedical Computing
The National Centers for Biomedical Computing (NCBCs) are part of the U.S. National Institutes of Health plan to develop and implement the core of a universal computing infrastructure that is urgently needed to speed progress in biomedical research. Their mission is to create innovative software programs and other tools that will enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. Recognizing the potential benefits to human health that can be realized from applying and advancing the field of biomedical computing, the Biomedical Information Science and Technology Initiative (BISTI) was launched at the NIH in April 2000. This initiative is aimed at making optimal use of computer science and technology to address problems in biology and medicine. The full text of the original BISTI Report is available. As of April 2016, the web site for the National Centers for Biomedical Computing (http://www.ncbcs.org) is no longer mana ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java (programming Language)
Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally developed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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