14,249 research outputs found
Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.
Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges--management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu
High-Performance Cloud Computing: A View of Scientific Applications
Scientific computing often requires the availability of a massive number of
computers for performing large scale experiments. Traditionally, these needs
have been addressed by using high-performance computing solutions and installed
facilities such as clusters and super computers, which are difficult to setup,
maintain, and operate. Cloud computing provides scientists with a completely
new model of utilizing the computing infrastructure. Compute resources, storage
resources, as well as applications, can be dynamically provisioned (and
integrated within the existing infrastructure) on a pay per use basis. These
resources can be released when they are no more needed. Such services are often
offered within the context of a Service Level Agreement (SLA), which ensure the
desired Quality of Service (QoS). Aneka, an enterprise Cloud computing
solution, harnesses the power of compute resources by relying on private and
public Clouds and delivers to users the desired QoS. Its flexible and service
based infrastructure supports multiple programming paradigms that make Aneka
address a variety of different scenarios: from finance applications to
computational science. As examples of scientific computing in the Cloud, we
present a preliminary case study on using Aneka for the classification of gene
expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape
NASA Thesaurus Supplement: A three part cumulative supplement to the 1982 edition of the NASA Thesaurus (supplement 3)
The three part cumulative NASA Thesaurus Supplement to the 1982 edition of the NASA Thesaurus includes Part 1, Hierarchical Listing, Part 2, Access Vocabulary, and Part 3, Deletions. The semiannual supplement gives complete hierarchies for new terms and includes new term indications for entries new to this supplement
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Image analysis and statistical inference in neuroimaging with R
R is a language and environment for statistical computing and graphics.
It can be considered an alternative implementation of the S language
developed in the 1970s and 1980s for data analysis and graphics (Becker and
Chambers, 1984; Becker et al., 1988). The R language is part of the GNU
project and offers versions that compile and run on almost every major
operating system currently available. We highlight several R packages built
specifically for the analysis of neuroimaging data in the context of
functional MRI, diffusion tensor imaging, and dynamic contrast-enhanced MRI.
We review their methodology and give an overview of their capabilities for
neuroimaging. In addition we summarize some of the current activities in the
area of neuroimaging software development in R
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