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LONI Pipeline
The LONI Pipeline is a free distributed system for designing, executing, monitoring and sharing scientific workflowsRex, D. E., Ma, J.Q., and Toga, A.W. (2003). "The LONI Pipeline Processing Environment." Neuroimage, 19(3), 1033-48.Rex, D. E., Shattuck, D. W., Woods, R. P., Narr, K. L., Luders, E., Rehm, K., Stolzner, S. E., Rottenberg, D. E., and Toga, A. W. (2004). "A meta-algorithm for brain extraction in MRI." NeuroImage, 23(2), 625–637 on grid computing architectures. Pipeline allows users to connect and run any number of different software tools, and conveniently visualize and download the results. Unlike other workflow processing environments, Pipeline does not require new tools and services to include or be built against the core Pipeline libraries. The Pipeline environment references all data, services and tools as external objects. This allows the Pipeline to run as a light-weight middleware, but at the same time, restrict the scope of its applications. For example, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ser ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FreeSurfer
FreeSurfer is a brain imaging software package originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve. Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer contains a set of programs with a common focus of analyzing magnetic resonance imaging (MRI) scans of brain tissue. It is an important tool in functional brain mapping and contains tools to conduct both volume based and surface based analysis. FreeSurfer includes tools for the reconstruction of topologically correct and geometrically accurate models of both the gray/white and pial surfaces, for measuring cortical thickness, surface area and folding, and for computing inter-subject registration based on the pattern of cortical folds. 57,541 copies of the FreeSurfer software package have been registered for use as of April 2022 and it is a core tool in the pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neuroimaging
Neuroimaging is the use of quantitative (computational) techniques to study the structure and function of the central nervous system, developed as an objective way of scientifically studying the healthy human brain in a non-invasive manner. Increasingly it is also being used for quantitative studies of brain disease and psychiatric illness. Neuroimaging is a highly multidisciplinary research field and is not a medical specialty. Neuroimaging differs from neuroradiology which is a medical specialty and uses brain imaging in a clinical setting. Neuroradiology is practiced by radiologists who are medical practitioners. Neuroradiology primarily focuses on identifying brain lesions, such as vascular disease, strokes, tumors and inflammatory disease. In contrast to neuroimaging, neuroradiology is qualitative (based on subjective impressions and extensive clinical training) but sometimes uses basic quantitative methods. Functional brain imaging techniques, such as functional magnet ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Workflow Applications
A workflow consists of an orchestrated and repeatable pattern of activity, enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms. From a more abstract or higher-level perspective, workflow may be considered a view or representation of real work. The flow being described may refer to a document, service, or product that is being transferred from one step to another. Workflows may be viewed as one fundamental building block to be combined with other parts of an organization's structure such as information technology, teams, projects and hierarchies. Historical development The development of the concept of a workflow occurred above a series of loosely defined, overlapping eras. Beginnings in manufacturing The modern history of workflows ca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Workflow Management Systems
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 i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
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] |
Laboratory Of Neuro Imaging
A laboratory (; ; colloquially lab) is a facility that provides controlled conditions in which scientific or technological research, experiments, and measurement may be performed. Laboratory services are provided in a variety of settings: physicians' offices, clinics, hospitals, and regional and national referral centers. Overview The organisation and contents of laboratories are determined by the differing requirements of the specialists working within. A physics laboratory might contain a particle accelerator or vacuum chamber, while a metallurgy laboratory could have apparatus for casting or refining metals or for testing their strength. A chemist or biologist might use a wet laboratory, while a psychologist's laboratory might be a room with one-way mirrors and hidden cameras in which to observe behavior. In some laboratories, such as those commonly used by computer scientists, computers (sometimes supercomputers) are used for either simulations or the analysis of data. Scienti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Health Informatics
Health informatics is the field of science and engineering that aims at developing methods and technologies for the acquisition, processing, and study of patient data, which can come from different sources and modalities, such as electronic health records, diagnostic test results, medical scans. The health domain provides an extremely wide variety of problems that can be tackled using computational techniques. Health informatics is a spectrum of multidisciplinary fields that includes study of the design, development and application of computational innovations to improve health care. The disciplines involved combines medicine fields with computing fields, in particular computer engineering, software engineering, information engineering, bioinformatics, bio-inspired computing, theoretical computer science, information systems, data science, information technology, autonomic computing, and behavior informatics. In academic institutions, medical informatics research focus on a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Analysis Of Functional NeuroImages
Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity. AFNI is an agglomeration of programs that can be used interactively or flexibly assembled for batch processing using shell script. The term ''AFNI'' refers both to the entire suite and to a particular interactive program often used for visualization. AFNI is actively developed by the NIMH Scientific and Statistical Computing Core and its capabilities are continually expanding. AFNI runs under many Unix-like operating systems that provide X11 and Motif libraries, including IRIX, Solaris, Linux, FreeBSD and OS X. Precompiled binaries are available for some platforms. AFNI is available for research use under the GNU General Public License, the included SVM-light component is non-commercial and non-distributable. AFNI now comprises over 300,000 lines of C source code, and a skilled C programmer can add inter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mac OS X
macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of desktop and laptop computers it is the Usage share of operating systems#Desktop and laptop computers, second most widely used desktop OS, after Microsoft Windows and ahead of ChromeOS. macOS succeeded the classic Mac OS, a Mac operating system with nine releases from 1984 to 1999. During this time, Apple cofounder Steve Jobs had left Apple and started another company, NeXT Computer, NeXT, developing the NeXTSTEP platform that would later be acquired by Apple to form the basis of macOS. The first desktop version, Mac OS X 10.0, was released in March 2001, with its first update, 10.1, arriving later that year. All releases from Mac OS X Leopard, Mac OS X 10.5 Leopard and after are UNIX 03 certified, with an exception for OS X Lion, OS X 10. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FMRIB Software Library
The FMRIB Software Library, abbreviated FSL, is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data. FSL is available as both precompiled binaries and source code for Apple and PC (Linux) computers. It is freely available for non-commercial use. FSL Functionality History and development FSL is written mainly by members of the FMRIB (Functional Magnetic Resonance Imaging of the Brain) Analysis Group, Oxford University, UK. The first release of FSL was in 2000; there has been approximately one major new release each year to date. The FMRIB Analysis Group is primarily funded by the Wellcome Trust and the UK EPSRC and MRC Research Councils. See also * AFNI * FreeSurfer * SPM * Neuroimaging Neuroimaging is the use of quantitative (computational) techniques to study the structure and function of the central nervous system, developed as an objective way of scientifically studying the healthy hum ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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