17863610
The theoretic center of computer science
In this article we examine computer science in general, and theory and distributed computing in particular. We present a map of the computer science conferences, speculating about the center of computer science. In addition we present some trends and developments. Finally we revisit centrality, wondering about the central actors in computer science. This article is a printed version of a frivolous PODC 2007 business meeting talk, held by the second author. In an attempt to address a broader audience we have extended the content by data about theory conferences and computer science in general. Still, the character of the information remains the same, meaning our investigations should not be taken too seriously.
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.
1441153
The Layered World of Scientific Conferences
Recent models have introduced the notion of dimensions and hierarchies in social networks. These models motivate the mining of small world graphs under a new perspective. We exemplary base our work on a conference graph, which is constructed from the DBLP publication records. We show that this graph indeed exhibits a layered structure as the models suggest. We then introduce a subtraction approach that allows to segregate layers. Using this technique we separate the conference graph into a thematic and a quality layer. As concrete applications of the discussed methods we present a novel rating method as well as a conference search tool that bases on our graph and its layer separation.
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.
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.
13966878
From Web to Map: Exploring the World of Music
Ever growing music collections ask for novel ways of organization. The traditional browsing of folder hierarchies or search by title and album tends to be insufficient to maintain an overview of a collection of orders of thousands of tracks. Methods based on song similarity offer an alternative to keyword-based search. In this work we propose to use a high-dimensional map of the "world of music" as a data structure for music retrieval and exploration of personal collections. Our approach does not require expensive analysis of audio signals and scales to hundreds of thousands of tracks. The techniques presented in this work can be used in a variety of applications, ranging from automatic DJs to file sharing on mobile devices. As a concrete example, we have developed a Web-application that allows users to visualize and navigate through their music collections and create playlists by specifying trajectories.
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.
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.
14065275
eggNOG: automated construction and annotation of orthologous groups of genes
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database (‘evolutionary genealogy of genes: Non-supervised Orthologous Groups’), which contains orthologous groups constructed from Smith–Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de.
6311275
STRING 8—a global view on proteins and their functional interactions in 630 organisms
Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein–protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. The most important new developments in STRING 8 over previous releases include a URL-based programming interface, which can be used to query STRING from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures. Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein–protein interactions currently available. STRING can be reached at http://string-db.org/.