Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid

Organizing and annotating biomedical data in structured ways has gained much interest and focus in the last 30 years. Driven by decreases in digital storage costs and advances in genetics sequencing, imaging, electronic data collection, and microarray technologies, data is being collected at an ever increasing rate. The need to store and exchange data in meaningful ways in support of data analysis, hypothesis testing and future collaborative use is pervasive. Because trans-disciplinary projects rely on effective use of data from many domains, there is a genuine interest in informatics community on how best to store and combine this data while maintaining a high level of data quality and documentation. The difficulties in sharing and combining raw data become amplified after post-processing and/or data analysis in which the new dataset of interest is a function of the original data and may have been collected by multiple collaborating sites. Simple meta-data, documenting which subject and version of data were used for a particular analysis, becomes complicated by the heterogeneity of the collecting sites yet is critically important to the interpretation and reuse of derived results. This manuscript will present a case study of using the XML-Based Clinical Experiment Data Exchange (XCEDE) schema and the Human Imaging Database (HID) in the Biomedical Informatics Research Network's (BIRN) distributed environment to document and exchange derived data. The discussion includes an overview of the data structures used in both the XML and the database representations, insight into the design considerations, and the extensibility of the design to support additional analysis streams

The influence of emotional distraction on verbal working memory: An fMRI investigation comparing individuals with schizophrenia and healthy adults

The ability to maintain information over short periods of time (i.e., working memory) is critically important in a variety of cognitive functions including language, planning, and decision-making. Recent functional Magnetic Resonance Imaging (fMRI) research with healthy adults has shown that brain activations evoked during the delay interval of working memory tasks can be reduced by the presentation of distracting emotional events, suggesting that emotional events may take working-memory processes momentarily offline. Both executive function and emotional processing are disrupted in schizophrenia, and here we sought to elucidate the effect of emotional distraction upon brain activity in schizophrenic and healthy adults performing a verbal working memory task. During the delay period between the memoranda and memory probe items, emotional and neutral distractors differentially influenced brain activity in these groups. In healthy adults, the hemodynamic response from posterior cingulate, orbital frontal cortex, and the parietal lobe strongly differentiated emotional from neutral distractors. In striking contrast, schizophrenic adults showed no significant differences in brain activation when processing emotional and neutral distractors. Moreover, the influence of emotional distractors extended into the memory probe period in healthy, but not schizophrenic, adults. The results suggest that although emotional items are highly salient for healthy adults, emotional items are no more distracting than neutral ones to individuals with schizophrenia

The Function Biomedical Informatics Research Network Data Repository

The Function Biomedical Informatics Research Network (FBIRN) developed methods and tools for conducting multi-scanner functional magnetic resonance imaging (fMRI) studies. Method and tool development were based on two major goals: 1) to assess the major sources of variation in fMRI studies conducted across scanners, including instrumentation, acquisition protocols, challenge tasks, and analysis methods, and 2) to provide a distributed network infrastructure and an associated federated database to host and query large, multi-site, fMRI and clinical datasets. In the process of achieving these goals the FBIRN test bed generated several multi-scanner brain imaging data sets to be shared with the wider scientific community via the BIRN Data Repository (BDR). The FBIRN Phase 1 dataset consists of a traveling subject study of 5 healthy subjects, each scanned on 10 different 1.5 to 4 Tesla scanners. The FBIRN Phase 2 and Phase 3 datasets consist of subjects with schizophrenia or schizoaffective disorder along with healthy comparison subjects scanned at multiple sites. In this paper, we provide concise descriptions of FBIRN’s multi-scanner brain imaging data sets and details about the BIRN Data Repository instance of the Human Imaging Database (HID) used to publicly share the data

Proceedings of the Sixth International Workshop on Web Caching and Content Distribution

OVERVIEW The International Web Content Caching and Distribution Workshop (WCW) is a premiere technical meeting for researchers and practitioners interested in all aspects of content caching, distribution and delivery on the Internet. The 2001 WCW meeting was held on the Boston University Campus. Building on the successes of the five previous WCW meetings, WCW01 featured a strong technical program and record participation from leading researchers and practitioners in the field. This report includes all the technical papers presented at WCW'01. Note: Proceedings of WCW'01 are published by Elsevier. Hardcopies of these proceedings can be purchased through the workshop organizers. As a service to the community, electronic copies of all WCW'01 papers are accessible through Technical Report BUCS‐TR‐2001‐017, available from the Boston University Computer Science Technical Report Archives at http://www.cs.bu.edu/techreps. [Ed.note: URL outdated. Use http://www.bu.edu/cs/research/technical-reports/ or http://hdl.handle.net/2144/1455 in this repository to access the reports.]Cisco Systems; InfoLibria; Measurement Factory Inc; Voler

Not All Hits Are Created Equal: Cooperative Proxy Caching Over a Wide-Area Network

Given the benefits of sharing a cache among large user populations, Internet Service Providers will likely enter into peering agreements to share their caches. This position paper describes our approach for inter-proxy cooperation in this environment. While existing cooperation models focus on maximizing global hit ratios, values of cache hits in our environment depend on peering agreements and access latency of various proxies. It may well be that obtaining an object directly from the Internet is less expensive and faster than from a distant cache. Our approach takes advantage of these distinctions to reduce the overhead for locating objects in the global cache. 1 Introduction Recent studies of Web access traces have showed significant benefits of providing a shared cache to a large user population. This prompted an active interest in large-scale distributed proxy caching platforms, in which multiple proxies cooperate and share the cached objects. Existing approaches to inter-proxy c..

Directory Structures for Scalable Internet Caches

Use of Internet caches is a cheap and effective way to improve performance for all Internet users. Distributed caches offer the potential to serve larger user communities and to deliver higher hit ratios on shared Web documents. The key to building effective distributed caches is a directory structure that allows individual caching servers to locate objects cached at neighboring sites, combining them into a logically unified collective cache. This paper uses Web traces to evaluate a range of alternatives for managing directories in distributed Internet caches. We use trace-driven executions and simulations of prototype caches to compare multicast-based queries of local maps (Harvest) with unicast queries of a global map (CRISP). We then use properties of the traces to predict performance of CRISP variants in which the global map is partitioned or replicated. Finally, we propose a novel lazy CRISP structure based on weakly consistent replication of the most valuable subset of the global..

A Taste of Crispy Squid

Distributed proxy caches are in use throughout the world to reduce access latency and bandwidth demands for Internet object transfer. The CRISP project seeks to build more effective distributed Web caches by exploring alternatives to the hierarchical structure and multicast handling of probes common to the most popular distributed Web cache systems. CRISP caches are structured as a collective of autonomous Web proxy servers sharing their cache directories through a common mapping service that can be queried with at most one message exchange. Individual servers may be configured to replicate all or part of the global map in order to balance access cost, overhead and hit ratio, depending on the size and geographic dispersion of the collective cache. We have prototyped several CRISP cache structures in Crispy Squid, an extension to the Squid Internet Object Cache. We are evaluating these cache structures using Proxycizer, a full-featured package for replaying traces of observed request tr..