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.
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.
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.
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.
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.
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/
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.
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.
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.