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Scientific Workflow 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. 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. Scientific workflow systems play an important role in enabling this vision. More specialized scientific workflow systems provide a visual programming front end enabling users to easily construct their applications as a visual graph by connecting nodes together, and tools have also been developed to build such applications in a platform-independent manner. Each directed edge in the graph of a workflow typically represents a connection from the output of one application to the input of the next. A sequence of such edges may be called a pipeline. A bioinfo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cuneiform (programming Language)
Cuneiform is an open-source workflow language for large-scale scientific data analysis. It is a statically typed functional programming language promoting parallel computing. It features a versatile foreign function interface allowing users to integrate software from many external programming languages. At the organizational level Cuneiform provides facilities like conditional branching and general recursion making it Turing-complete. In this, Cuneiform is the attempt to close the gap between scientific workflow systems like Taverna, KNIME, or Galaxy and large-scale data analysis programming models like MapReduce or Pig Latin while offering the generality of a functional programming language. Cuneiform is implemented in distributed Erlang. If run in distributed mode it drives a POSIX-compliant distributed file system like Gluster or Ceph (or a FUSE integration of some other file system, e.g., HDFS). Alternatively, Cuneiform scripts can be executed on top of HTCondor or Hadoo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
YAML
YAML ( and ) (''see '') 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 which intentionally differs from Standard Generalized Markup Language (SGML). It uses both Python-style indentation to indicate nesting, and a more compact format that uses for lists and for maps thus JSON files are valid YAML 1.2. 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. 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: [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JSON
JSON (JavaScript Object Notation, pronounced ; also ) is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays (or other serializable values). It is a common data format with diverse uses in electronic data interchange, including that of web applications with servers. JSON is a 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. Any valid JSON file is a valid JavaScript (.js) file, even though it makes no changes to a web page on its own. Douglas Crockford originally specified the JSON format in the early 2000s. 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) specifies "Pronounced , as in ' Jason and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Collective Knowledge (software)
The Collective Knowledge (CK) project is an open-source framework and 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 components and automation actions with unified JSON API, JSON meta information, and a UID based on FAIR principles * assemble portable workflows from shared components (such as multi-objective autotuning and Design space exploration) * automate, crowdsource and reproduce benchmarking of complex computational systems * unify predictive analytics (scikit-learn, R, DNN) * enable reproducible and interactive papers Notable usages * ARM uses CK to accelerate computer engineering * Association for Computing Machinery evaluates CK for possible integration with the ACM Digital Library sponsored by the Sloan Foundation and fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
BioBIKE
BioBike(nee. BioLingua ) is a cloud-based, through-the-web programmable ( Paas) symbolic biocomputing and bioinformatics platform that aims to make computational biology, and especially intelligent biocomputing (that is, the application of 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-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 system in which all objects, data, and knowledge are represented. This enables code written either in the native Lisp, in the visual programming language, or systems of rules expressed in the SNARK theorem prover to access the whole of biological knowledge in an integrated manner. For its time (released in 2002) it wa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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. S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 Python ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache Airavata
Airavata is a 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. 2011. ''Apache 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 http://doi.acm.org/10.1145/2110486.2110490 Retrieved 15 February 2012 Airavata consists of four components: [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
