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Bioinformatics Workflow Management System
A scientific workflow system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or workflow, in a scientific application. Scientific workflow systems are generally developed for use by scientists from different disciplines like astronomy, earth science, and bioinformatics. 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. Applications Distributed scientists can collaborate on conducting large scale scientific experiments and knowledge discovery applications using distributed systems of computing resources, data sets, and devices. S ... [...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 the 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 allows 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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 had a SPARQL Endpoint, with an interactive tutorial. Origin The myExperiment project was initially directed by David De Roure at University of Southampton (later University of Oxford) and was 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 Capturing digital experiments While the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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YAML
YAML ( ) is a human-readable data serialization language. It is commonly used for configuration files and in applications where data is being stored or transmitted. YAML targets many of the same communications applications as Extensible Markup Language (XML) but has a minimal syntax that intentionally differs from Standard Generalized Markup Language (SGML). It uses Python-style indentation to indicate nesting and does not require quotes around most string values (it also supports JSON style and mixed in the same file). Custom data types are allowed, but YAML natively encodes scalars (such as strings, integers, and floats), lists, and associative arrays (also known as maps, dictionaries or hashes). These data types are based on the Perl programming language, though all commonly used high-level programming languages share very similar concepts. The colon-centered syntax, used for expressing key-value pairs, is inspired by electronic mail headers as defined in , and the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Common Workflow Language
The Common Workflow Language (CWL) is a standard for describing computational data-analysis workflows. Development of CWL is focused particularly on serving the data-intensive sciences, such as bioinformatics, medical imaging, astronomy, physics, and chemistry. Standard A key goal of the CWL is to allow the creation of a workflow that is portable and thus may be run reproducibly in different computational environments. The CWL originated from discussions in 2014 betweePeter Amstutz an Michael R. Crusoe (at that time their respective affiliations were: |
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JSON
JSON (JavaScript Object Notation, pronounced or ) is an open standard file format and electronic data interchange, data interchange format that uses Human-readable medium and data, human-readable text to store and transmit data objects consisting of name–value pairs and array data type, arrays (or other serialization, serializable values). It is a commonly used data format with diverse uses in electronic data interchange, including that of web applications with server (computing), servers. JSON is a Language-independent specification, language-independent data format. It was derived from JavaScript, but many modern programming languages include code to generate and parse JSON-format data. JSON filenames use the extension .json. Douglas Crockford originally specified the JSON format in the early 2000s. Transcript: He and Chip Morningstar sent the first JSON message in April 2001. Naming and pronunciation The 2017 international standard (ECMA-404 and ISO/IEC 21778:2017) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Collective Knowledge (software)
The Collective Knowledge (CK) project is an open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ... software framework, framework and software repository, repository to enable collaborative, reproducible and sustainable research and development of complex computational systems. CK is a small, portable, customizable and decentralized infrastructure helping researchers and practitioners: * share their code, data and models as reusable Python (programming language), Python components and automation actions with unified JSON API, JSON meta information, and a Unique identifier, UID based on FAIR data, FAIR principles * assemble portable workflows from shared components (such as multi-objective autotuning and Design space exploration) * automate, crowdsource and reproduce benchmar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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). About Biclipse 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. Product 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 col ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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BioBIKE
BioBike(nee. BioLingua ) is a Cloud computing, cloud-based, through-the-web programmable (platform as a service, Paas) symbolic biocomputing and bioinformatics platform that aims to make computational biology, and especially intelligent biocomputing (that is, the application of artificial intelligence, Artificial Intelligence to computational biology) accessible to research scientists who are not expert programmers. Unique capabilities BioBIKE is an integrated symbolic biocomputing and bioinformatics platform, built from the start as an entirely (what is now called) Cloud computing, cloud-based architecture where all computing is done in remote servers, and all user access is accomplished through web browsers. BioBIKE has a built-in Frame language, frame system in which all objects, data, and knowledge are represented. This enables code written either in the native Lisp (programming language), Lisp, in the visual programming language, or systems of rules expressed in the SNARK ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Apache Taverna
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 Software Foundation incubator. Taverna allowed users to integrate many different software components, including web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Data Bank 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. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Apache Airflow
Apache Airflow is an open-source workflow management platform for data engineering pipelines. It started at Airbnb in October 2014 as a solution to manage the company's increasingly complex workflows. Creating Airflow allowed Airbnb to programmatically author and schedule their workflows and monitor them via the built-in Airflow user interface. From the beginning, the project was made open source, becoming an Apache Incubator project in March 2016 and a top-level Apache Software Foundation project in January 2019. Airflow is written in Python, and workflows are created via Python scripts. Airflow is designed under the principle of "configuration as code". While other "configuration as code" workflow platforms exist using markup languages like XML, using Python allows developers to import libraries and classes to help them create their workflows. Overview Airflow uses directed acyclic graphs (DAGs) to manage workflow orchestration. Tasks and dependencies are defined in P ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Apache Airavata
Airavata is an open source software suite that composes, manages, executes, and monitors large-scale applications and workflows on computational resources, ranging from local clusters to national grids, and computing clouds.Suresh Marru, Lahiru Gunathilake, Chathura Herath, Patanachai Tangchaisin, Marlon Pierce, Chris Mattmann, Raminder Singh, Thilina Gunarathne, Eran Chinthaka, Ross Gardler, Aleksander Slominski, Ate Douma, Srinath Perera, and Sanjiva Weerawarana. 2011Apache airavata: a framework for distributed applications and computational workflows In Proceedings of the 2011 ACM workshop on Gateway computing environments (GCE '11). ACM, New York, NY, USA, 21-28. DOI 10.1145/2110486.2110490. Retrieved 15 February 2012 Components Airavata consists of four components:[...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Anduril (workflow Engine)
Anduril is an open source component-based workflow framework for scientific data analysis developed at the Systems Biology Laboratory, University of Helsinki. Anduril is designed to enable systematic, flexible and efficient data analysis, particularly in the field of high-throughput experiments in biomedical research. The workflow system currently provides components for several types of analysis such as DNA sequencing#High-throughput sequencing, sequencing, gene expression, Single-nucleotide polymorphism, SNP, ChIP-on-chip, Array comparative genomic hybridization, comparative genomic hybridization and exon microarray analysis as well as cytometry and Image analysis, cell imaging analysis. Architecture and features A workflow is a series of processing steps connected together so that the output of one step is used as the input of another. Processing steps implement data analysis tasks such as data importing, statistical tests and report generation. In Anduril, processing steps ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |