11733134
Community-Aware Mobile Networking
Community related applications such as dating platforms, instant messengers, or file-sharing tools enjoy a great popularity in the Internet. Motivated by this success, community-awareness also has become a hot topic in the mobile world. Despite considerable efforts, however, mobile solutions still cannot compete with their Internet counterparts. A key feature of community-aware applications is profile matching. To a large extent, the missing popularity of mobile approaches can be explained with the problems traditional one-to-one keyword matching causes in a purely decentralized environment: Expressive keywords are unlikely to match because of a lack in user density, and a superficial keyword classification misses the application needs. Hence, we face the challenge to compare characteristic topics in purely mobile applications. To address this challenge, this paper presents a fundamentally new matching scheme based on a combination of topology analysis and distance labeling. Proof-of-concept experiments demonstrate that the proposed scheme has indeed the potential to facilitate the comparison of highly specialized keywords in mobile environments.
8826212
Distributed asymmetric verification in computational grids
Lucrative incentives in grid computing do not only attract honest participants, but also cheaters. To prevent selfish behavior, verification mechanisms are required. Today's solutions mostly base on redundancy and inherently exhibit a considerable overhead. Often, however, the verification of a result takes much less time than its computation. In this paper we propose a distributed checking scheme that exploits this asymmetry. Our mechanism detects wrong results and excludes cheaters in a distributed manner and hence disburdens the central of the grid server. We show how the verification scheme is used in an application which aims at breaking the discrete logarithm problem by a parallel implementation of the Pollard-p algorithm. Our implementation extends the BOINC server software and is robust to various rational attacks even in the presence of colluders.
195351395
Layers and Hierarchies in Real Virtual Networks
6933069
Cluestr: mobile social networking for enhanced group communication
Recent technological advances foster the spreading of social software in the mobile domain. Hence, future usage patterns of mobile devices will involve more group interaction. While collaboration using mobile devices is an active area of research, only limited attention has been paid to the efficient initiation of group communication from mobile terminals. In this paper we present a community-aware mechanism that allows to efficiently select contacts in order to address them as a group. We have integrated the proposed method into a proof-of-concept application, and present preliminary experiments that demonstrate the accuracy of the approach and show significant time savings in the group initialization process.
7026402
Exploring music collections on mobile devices
Ever larger collections of music are stored on mobile devices. The process of managing these repositories therefore becomes increasingly challenging. In this work we propose to use a map of the "world of music" as a data structure for music exploration and retrieval on mobile devices. We present Mobile Music Explorer---a mobile application, which allows users to create playlists by specifying trajectories on the map and to use similarity based search methods to navigate through their personal music collections. Our navigation methods ensure that any part of the collection can quickly be reached, even for a large set of items. Moreover, we show that the map representation is a natural approach to provide efficient and distributed operation.
2870781
Visually and Acoustically Exploring the High-Dimensional Space of Music
The permanent growth of personal music collections caused by the ongoing digital revolution asks for novel ways of organization. Traditional list based approaches are---particularly for use in mobile devices---no longer appropriate. In this paper we discuss two alternative exploration schemes, both taking advantage of a recently proposed high-dimensional music similarity space. First, we present an interface that facilitates visual navigation through a collection. Then, we propose the use of an acoustic approach, which adapts to the user's taste. The proposed solutions have been integrated into an Android based prototype application. The conducted user experiments indicate that both methods outperform alternative approaches that head into similar directions.
7864638
SuperTarget and Matador: resources for exploring drug-target relationships
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins. An easy-to-use query interface enables the user to pose complex queries, for example to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target the same protein but are metabolized by different enzymes. Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador. SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de
18978594
Directory-Based Metadata Optimizations for Small Files in PVFS
Modern file systems maintain extensive metadata about stored files. While this usually is useful, there are situations when the additional overhead of such a design becomes a problem in terms of performance. This is especially true for parallel and cluster file systems, because due to their design every metadata operation is even more expensive. 
 
In this paper several changes made to the parallel cluster file system PVFS are presented. The changes are targeted at the optimization of workloads with large numbers of small files. To improve metadata performance, PVFS was modified such that unnecessary metadata is not managed anymore. 
 
Several tests with a large quantity of files were done to measure the benefits of these changes. The tests have shown that common file system operations can be sped up by a factor of two even with relatively few changes.
2622646
STITCH: interaction networks of chemicals and proteins
The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH (‘search tool for interactions of chemicals’) integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug–target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/
2031555
OnTheFly: a tool for automated document-based text annotation, data linking and network generation
OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database. Availability: http://onthefly.embl.de, http://onthefly.embl.de/FAQ.html Contact: pavlopou@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
18262140
Dynamic file system semantics to enable metadata optimizations in PVFS
Modern file systems maintain extensive metadata about stored files. While metadata typically is useful, there are situations when the additional overhead of such a design becomes a problem in terms of performance. This is especially true for parallel and cluster file systems, where every metadata operation is even more expensive due to their architecture. In this paper several changes made to the parallel cluster file system Parallel Virtual File System (PVFS) are presented. The changes target at the optimization of workloads with large numbers of small files. To improve the metadata performance, PVFS was modified such that unnecessary metadata is not managed anymore. Several tests with a large quantity of files were performed to measure the benefits of these changes. The tests have shown that common file system operations can be sped up by a factor of two even with relatively few changes. Copyright © 2009 John Wiley & Sons, Ltd.