NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

Theory and Practice of Data Citation

Citations are the cornerstone of knowledge propagation and the primary means of assessing the quality of research, as well as directing investments in science. Science is increasingly becoming "data-intensive", where large volumes of data are collected and analyzed to discover complex patterns through simulations and experiments, and most scientific reference works have been replaced by online curated datasets. Yet, given a dataset, there is no quantitative, consistent and established way of knowing how it has been used over time, who contributed to its curation, what results have been yielded or what value it has. The development of a theory and practice of data citation is fundamental for considering data as first-class research objects with the same relevance and centrality of traditional scientific products. Many works in recent years have discussed data citation from different viewpoints: illustrating why data citation is needed, defining the principles and outlining recommendations for data citation systems, and providing computational methods for addressing specific issues of data citation. The current panorama is many-faceted and an overall view that brings together diverse aspects of this topic is still missing. Therefore, this paper aims to describe the lay of the land for data citation, both from the theoretical (the why and what) and the practical (the how) angle.Comment: 24 pages, 2 tables, pre-print accepted in Journal of the Association for Information Science and Technology (JASIST), 201

V2X Content Distribution Based on Batched Network Coding with Distributed Scheduling

Content distribution is an application in intelligent transportation system to assist vehicles in acquiring information such as digital maps and entertainment materials. In this paper, we consider content distribution from a single roadside infrastructure unit to a group of vehicles passing by it. To combat the short connection time and the lossy channel quality, the downloaded contents need to be further shared among vehicles after the initial broadcasting phase. To this end, we propose a joint infrastructure-to-vehicle (I2V) and vehicle-to-vehicle (V2V) communication scheme based on batched sparse (BATS) coding to minimize the traffic overhead and reduce the total transmission delay. In the I2V phase, the roadside unit (RSU) encodes the original large-size file into a number of batches in a rateless manner, each containing a fixed number of coded packets, and sequentially broadcasts them during the I2V connection time. In the V2V phase, vehicles perform the network coded cooperative sharing by re-encoding the received packets. We propose a utility-based distributed algorithm to efficiently schedule the V2V cooperative transmissions, hence reducing the transmission delay. A closed-form expression for the expected rank distribution of the proposed content distribution scheme is derived, which is used to design the optimal BATS code. The performance of the proposed content distribution scheme is evaluated by extensive simulations that consider multi-lane road and realistic vehicular traffic settings, and shown to significantly outperform the existing content distribution protocols.Comment: 12 pages and 9 figure

Taxonomy of P2P Applications

Peer-to-peer (p2p) networks have gained immense popularity in recent years and the number of services they provide continuously rises. Where p2p-networks were formerly known as file-sharing networks, p2p is now also used for services like VoIP and IPTV. With so many different p2p applications and services the need for a taxonomy framework rises. This paper describes the available p2p applications grouped by the services they provide. A taxonomy framework is proposed to classify old and recent p2p applications based on their characteristics

Dynamic analysis of an institutional conflict within the music industry

Peer-to-peer technology has made massive music piracy possible, which, in turn, has arguably had a significant economic impact on the recording industry. Record labels have responded to online piracy with litigation and are also considering self-help measures. It is currently not obvious whether or not these counter-piracy strategies will ultimately stifle online file sharing in the long term. With this paper we attempt to add to our understanding of the conflict within the institution that is the commercial music industry. We conduct an institutional analysis of the industry in transition and extend the traditional pattern modeling methodology with a formal resource-based model of a representative online music network. The model accounts for complex causal interactions between resources, private provision of common goods, free riding and membership dynamics. The numerical implementation of the model is the basis of a decision support system, which is used in a series of computer experiments that emulate anti-piracy scenarios. We show that a peer-to-peer system may be quite resilient to outside disturbances. The experiments also demonstrate that policies rank differently in their effectiveness based on a selected yardstick.Peer-to-peer (P2P) networks; Online File Sharing; Copyright; Simulation

Learning Parallel Computations with ParaLab

In this paper, we present the ParaLab teachware system, which can be used for learning the parallel computation methods. ParaLab provides the tools for simulating the multiprocessor computational systems with various network topologies, for carrying out the computational experiments in the simulation mode, and for evaluating the efficiency of the parallel computation methods. The visual presentation of the parallel computations taking place in the computational experiments is the key feature of the system. ParaLab can be used for the laboratory training within various teaching courses in the field of parallel, distributed, and supercomputer computations