Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Using Visualization to Support Data Mining of Large Existing Databases

In this paper. we present ideas how visualization technology can be used to improve the difficult process of querying very large databases. With our VisDB system, we try to provide visual support not only for the query specification process. but also for evaluating query results and. thereafter, refining the query accordingly. The main idea of our system is to represent as many data items as possible by the pixels of the display device. By arranging and coloring the pixels according to the relevance for the query, the user gets a visual impression of the resulting data set and of its relevance for the query. Using an interactive query interface, the user may change the query dynamically and receives immediate feedback by the visual representation of the resulting data set. By using multiple windows for different parts of the query, the user gets visual feedback for each part of the query and, therefore, may easier understand the overall result. To support complex queries, we introduce the notion of approximate joins which allow the user to find data items that only approximately fulfill join conditions. We also present ideas how our technique may be extended to support the interoperation of heterogeneous databases. Finally, we discuss the performance problems that are caused by interfacing to existing database systems and present ideas to solve these problems by using data structures supporting a multidimensional search of the database

A load-sharing architecture for high performance optimistic simulations on multi-core machines

In Parallel Discrete Event Simulation (PDES), the simulation model is partitioned into a set of distinct Logical Processes (LPs) which are allowed to concurrently execute simulation events. In this work we present an innovative approach to load-sharing on multi-core/multiprocessor machines, targeted at the optimistic PDES paradigm, where LPs are speculatively allowed to process simulation events with no preventive verification of causal consistency, and actual consistency violations (if any) are recovered via rollback techniques. In our approach, each simulation kernel instance, in charge of hosting and executing a specific set of LPs, runs a set of worker threads, which can be dynamically activated/deactivated on the basis of a distributed algorithm. The latter relies in turn on an analytical model that provides indications on how to reassign processor/core usage across the kernels in order to handle the simulation workload as efficiently as possible. We also present a real implementation of our load-sharing architecture within the ROme OpTimistic Simulator (ROOT-Sim), namely an open-source C-based simulation platform implemented according to the PDES paradigm and the optimistic synchronization approach. Experimental results for an assessment of the validity of our proposal are presented as well