Statistical computations with AstroGrid and the Grid

We outline our first steps towards marrying two new and emerging technologies; the Virtual Observatory (e.g, Astro- Grid) and the computational grid. We discuss the construction of VOTechBroker, which is a modular software tool designed to abstract the tasks of submission and management of a large number of computational jobs to a distributed computer system. The broker will also interact with the AstroGrid workflow and MySpace environments. We present our planned usage of the VOTechBroker in computing a huge number of n–point correlation functions from the SDSS, as well as fitting over a million CMBfast models to the WMAP data.

Cloud computing in e-science: research challenges and opportunities

SOA (Service Oriented Architecture), workflow, the Semantic Web, and Grid computing are key enabling information technologies in the development of increasingly sophisticated e-Science infrastructures and application platforms. While the emergence of Cloud computing as a new computing paradigm has provided new directions and opportunities for e-Science infrastructure development, it also presents some challenges. Scientific research is increasingly finding that it is difficult to handle “big data” using traditional data processing techniques. Such challenges demonstrate the need for a comprehensive analysis on using the above mentioned informatics techniques to develop appropriate e-Science infrastructure and platforms in the context of Cloud computing. This survey paper describes recent research advances in applying informatics techniques to facilitate scientific research particularly from the Cloud computing perspective. Our particular contributions include identifying associated research challenges and opportunities, presenting lessons learned, and describing our future vision for applying Cloud computing to e-Science. We believe our research findings can help indicate the future trend of e-Science, and can inform funding and research directions in how to more appropriately employ computing technologies in scientific research. We point out the open research issues hoping to spark new development and innovation in the e-Science field.

K-Surfer: a KNIME extension for the management and analysis of Human brain MRI FreeSurfer/FSL data

Human brain imaging techniques, such as Magnetic Resonance Imaging (MRI) or Diffusion Tensor Imaging (DTI), have been established as scientific and diagnostic tools and their adoption is growing in popularity. Statistical methods, machine learning and data mining algorithms have successfully been adopted to extract predictive and descriptive models from neuroimage data. However, the knowledge discovery process typically requires also the adoption of pre-processing, post-processing and visualisation techniques in complex data workflows. Currently, a main problem for the integrated preprocessing and mining of MRI data is the lack of comprehensive platforms able to avoid the manual invocation of preprocessing and mining tools, that yields to an error-prone and inefficient process. In this work we present K-Surfer, a novel plug-in of the Konstanz Information Miner (KNIME) workbench, that automatizes the preprocessing of brain images and leverages the mining capabilities of KNIME in an integrated way. K-Surfer supports the importing, filtering, merging and pre-processing of neuroimage data from FreeSurfer, a tool for human brain MRI feature extraction and interpretation. K-Surfer automatizes the steps for importing FreeSurfer data, reducing time costs, eliminating human errors and enabling the design of complex analytics workflow for neuroimage data by leveraging the rich functionalities available in the KNIME workbench.

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.