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
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.
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.
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
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.
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.