A network approach for managing and processing big cancer data in clouds

Translational cancer research requires integrative analysis of multiple levels of big cancer data to identify and treat cancer. In order to address the issues that data is decentralised, growing and continually being updated, and the content living or archiving on different information sources partially overlaps creating redundancies as well as contradictions and inconsistencies, we develop a data network model and technology for constructing and managing big cancer data. To support our data network approach for data process and analysis, we employ a semantic content network approach and adopt the CELAR cloud platform. The prototype implementation shows that the CELAR cloud can satisfy the on-demanding needs of various data resources for management and process of big cancer data

AAPOR Report on Big Data

In recent years we have seen an increase in the amount of statistics in society describing different phenomena based on so called Big Data. The term Big Data is used for a variety of data as explained in the report, many of them characterized not just by their large volume, but also by their variety and velocity, the organic way in which they are created, and the new types of processes needed to analyze them and make inference from them. The change in the nature of the new types of data, their availability, the way in which they are collected, and disseminated are fundamental. The change constitutes a paradigm shift for survey research.There is a great potential in Big Data but there are some fundamental challenges that have to be resolved before its full potential can be realized. In this report we give examples of different types of Big Data and their potential for survey research. We also describe the Big Data process and discuss its main challenges

Digital Preservation Services : State of the Art Analysis

Research report funded by the DC-NET project.An overview of the state of the art in service provision for digital preservation and curation. Its focus is on the areas where bridging the gaps is needed between e-Infrastructures and efficient and forward-looking digital preservation services. Based on a desktop study and a rapid analysis of some 190 currently available tools and services for digital preservation, the deliverable provides a high-level view on the range of instruments currently on offer to support various functions within a preservation system.European Commission, FP7peer-reviewe

Consequences of refining biological networks through detailed pathway information : From genes to proteoforms

Biologiske nettverk kan brukes til å modellere molekylære prosesser, forstå sykdomsprogresjon og finne nye behandlingsstrategier. Denne avhandlingen har undersøkt hvordan utformingen av slike nettverk påvirker deres struktur, og hvordan dette kan benyttes til å forbedre spesifisiteten for påfølgende analyser av slike modeller. Det første som ble undersøkt var potensialet ved å bruke mer detaljerte molekylære data når man modellerer humane biokjemiske reaksjonsnettverk. Resultatene bekrefter at det er nok informasjon om proteoformer, det vil si proteiner i spesifikke post-translasjonelle tilstander, for systematiske analyser og viste også store forskjeller i strukturen mellom en gensentrisk og en proteoformsentrisk representasjon. Deretter utviklet vi programmatisk tilgang og søk i slike nettverk basert på ulike typer av biomolekyler, samt en generisk algoritme som muliggjør fleksibel kartlegging av eksperimentelle data knyttet til den teoretiske representasjonen av proteoformer i referansedatabaser. Til slutt ble det konstruert såkalte pathway-spesifikke nettverk ved bruk av ulike detaljnivåer ved representasjonen av biokjemiske reaksjoner. Her ble informasjon som vanligvis blir oversett i standard nettverksrepresentasjoner inkludert: små molekyler, isoformer og modifikasjoner. Strukturelle egenskaper, som nettverksstørrelse, graddistribusjon og tilkobling i både globale og lokale undernettverk, ble deretter analysert for å kvantifisere virkningene av endringene.Biological networks can be used to model molecular processes, understand disease progression, and find new treatment strategies. This thesis investigated how refining the design of biological networks influences their structure, and how this can be used to improve the specificity of pathway analyses. First, we investigate the potential to use more detailed molecular data in current human biological pathways. We verified that there are enough proteoform annotations, i.e. information about proteins in specific post-translational states, for systematic analyses and characterized the structure of gene-centric versus proteoform-centric network representations of pathways. Next, we enabled the programmatic search and mining of pathways using different models for biomolecules including proteoforms. We notably designed a generic proteoform matching algorithm enabling the flexible mapping of experimental data to the theoretic representation in reference databases. Finally, we constructed pathway-based networks using different degrees of detail in the representation of biochemical reactions. We included information overlooked in most standard network representations: small molecules, isoforms, and post-translational modifications. Structural properties such as network size, degree distribution, and connectivity in both global and local subnetworks, were analysed to quantify the impact of the added molecular entities.Doktorgradsavhandlin

2011 Strategic roadmap for Australian research infrastructure

The 2011 Roadmap articulates the priority research infrastructure areas of a national scale (capability areas) to further develop Australia’s research capacity and improve innovation and research outcomes over the next five to ten years. The capability areas have been identified through considered analysis of input provided by stakeholders, in conjunction with specialist advice from Expert Working Groups   It is intended the Strategic Framework will provide a high-level policy framework, which will include principles to guide the development of policy advice and the design of programs related to the funding of research infrastructure by the Australian Government. Roadmapping has been identified in the Strategic Framework Discussion Paper as the most appropriate prioritisation mechanism for national, collaborative research infrastructure. The strategic identification of Capability areas through a consultative roadmapping process was also validated in the report of the 2010 NCRIS Evaluation. The 2011 Roadmap is primarily concerned with medium to large-scale research infrastructure. However, any landmark infrastructure (typically involving an investment in excess of $100 million over five years from the Australian Government) requirements identified in this process will be noted. NRIC has also developed a ‘Process to identify and prioritise Australian Government landmark research infrastructure investments’ which is currently under consideration by the government as part of broader deliberations relating to research infrastructure. NRIC will have strategic oversight of the development of the 2011 Roadmap as part of its overall policy view of research infrastructure

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is ‘hidden’ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community