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Bioinformatics Workflow Management System
A bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, that relate to bioinformatics. There are currently many different workflow systems. Some have been developed more generally as scientific workflow systems for use by scientists from many different disciplines like astronomy and earth science. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed graph, where each node represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides a visual front-end, allowing the user to build and modify complex applications with little or no programming expertise. Examples In alphabetical order, some examples of bioinformatics workflow management systems include: * Anduril bioinformatics and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Workflow Management System
A workflow management system (WfMS or WFMS) provides an infrastructure for the set-up, performance and monitoring of a defined sequence of tasks, arranged as a workflow application. International standards There are several international standards-setting bodies in the field of workflow management: * Workflow Management Coalition * World Wide Web Consortium * Organization for the Advancement of Structured Information Standards * WS-BPEL 2.0 (integration-centric) and WS-BPEL4People (human task-centric) published by OASIS Standards Body. The underlying theoretical basis of workflow management is the mathematical concept of a Petri net. Each of the workflow models has tasks (nodes) and dependencies between the nodes. Tasks are activated when the dependency conditions are fulfilled. Workflows for people WfMS allow the user to define different workflows for different types of jobs or processes. For example, in a manufacturing setting, a design document might be automatically routed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Discovery Net
Discovery Net is one of the earliest examples of a scientific workflow system allowing users to coordinate the execution of remote services based on Web service and Grid Services (OGSA and Open Grid Services Architecture) standards. The system was designed and implemented at Imperial College London as part of the Discovery Net pilot project funded by the UK e-Science Programme (). Many of the concepts pioneered by Discovery Net have been later incorporated into a variety of other scientific workflow systems. History: The Discovery Net e-Science Pilot Project The Discovery Net system was developed as part of the Discovery Net pilot project (2001–2005), a £2m research project funded by the EPSRC under the UK e-Science Programme (). The research on the project was conducted at Imperial College London as a collaboration between the Departments of Computing, Physics, Biochemistry and Earth Science & Engineering. Being a single institution project, the project was unique compared ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Business Process Execution Language
The Web Services Business Process Execution Language (WS-BPEL), commonly known as BPEL (Business Process Execution Language), is an OASIS standard executable language for specifying actions within business processes with web services. Processes in BPEL export and import information by using web service interfaces exclusively. Overview One can describe Web-service interactions in two ways: as executable business processes and as abstract business processes. # An ''executable business process'': models an actual behavior of a participant in a business interaction. # An ''abstract business process'': is a partially specified process that is not intended to be executed. Contrary to Executable Processes, an Abstract Process may hide some of the required concrete operational details. Abstract Processes serve a descriptive role, with more than one possible use case, including observable behavior and/or process template. WS-BPEL aims to model the behavior of processes, via a lan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Kepler Scientific Workflow System
Kepler is a free software system for designing, executing, reusing, evolving, archiving, and sharing scientific workflows.Ludäscher B., Altintas I., Berkley C., Higgins D., Jaeger-Frank E., Jones M., Lee E., Tao J., Zhao Y. 2006. Scientific Workflow Management and the Kepler System. Special Issue: Workflow in Grid Systems. Concurrency and Computation: Practice & Experience 18(10): 1039-1065.Altintas I, Berkley C, Jaeger E, Jones M, Ludäscher B, Mock S. 2004. Kepler: An Extensible System for Design and Execution of Scientific Workflows. Proceedings of the Future of Grid Data Environments, Global Grid Forum 10.Michener, William K., James H. Beach, Matthew B. Jones, Bertram Ludaescher, Deana D. Pennington, Ricardo S. Pereira, Arcot Rajasekar, and Mark Schildhauer. 2007. "A Knowledge Environment for the Biodiversity and Ecological Sciences", Journal of Intelligent Information Systems, 29(1): 111-126. Kepler's facilities provide process and data monitoring, provenance information, an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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VisTrails
VisTrails is a scientific workflow management system developed at the Scientific Computing and Imaging Institute at the University of Utah that provides support for data exploration and visualization. It is written in Python and employs Qt via PyQt bindings. The system is open source, released under the GPL v2 license. The pre-compiled versions for Windows, Mac OS X, and Linux come with an installer and several packages, including VTK, matplotlib, and ImageMagick. VisTrails also supports user-defined packages. Overview VisTrails is a new system that provides provenance management support for exploratory computational tasks. It combines features of workflow and visualization systems. Similar to workflow systems, it allows the combination of loosely coupled resources, specialized libraries, and grid and Web services. Similar to some visualization systems, it provides a mechanism for parameter exploration and comparison of different results. But unlike these other systems, VisTrai ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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UGENE
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2. UGENE helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g., a lab database). UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE provides a graphical user interface (GUI) for the pre-built tools so biologists with no computer programming skills can access those tools more easily. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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] |
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OnlineHPC
The OnlineHPC was a free public web service that supplied tools to deal with high performance computers and online workflow editor. OnlineHPC allowed users to design and execute workflows using the online workflow designer and to work with high performance computers – clusters and clouds. Access to high performance resources was available as directly from the service user interface, as from workflow components. The workflow engine of the OnlineHPC service was Taverna as traditionally used for scientific workflow execution in such domains, as bioinformatics, cheminformatics, medicine, astronomy, social science, music, and digital preservation. History OnlineHPC was started at the Institute for Information Transmission Problems in 2012 as a project for the institute’s researchers whose work need access to computer clusters and who are not professional programmers. The project motivation is that there is a gap between researcher skills and competence level needed to run hi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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 engine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of ''individual'' genes and their roles in inheritance, genomics aims at the collective characterization and quantification of ''all'' of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Galaxy (computational Biology)
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system. Functionality Galaxy is a scientific workflow system. These systems provide a means to build multi-step computational analyses akin to a recipe. They typically provide a graphical user interface for specifying what data to operate on, what steps to take, and what order to do them in. Galaxy is also a data integration platform for biological data. It supports data uploads from the user's computer, by URL, and directly from many online resources (such as the UCSC Genome Browser, BioMart and InterMine). Galaxy supports a range of widely used biological data ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |