Challenges for Modeling and Simulation Methods in Systems Biology

Systems Biology is aimed at analyzing the behavior and interrelationships of biological systems and is characterized by combining experimentation, theory, and computation. Dedicated to exploring current challenges, the panel brings together people from a variety of disciplines whose perspectives illuminate diverse facets of Systems Biology and the challenges for modeling and simulation methods

Data access and integration in the ISPIDER proteomics grid

Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources

Web Server for Protein Interaction Searching

Tato práce se zabývá zbůsoby, jimiž je možné získávat data z bioinformatických databází obsahujících data týkajících se interakcí mezi proteiny. Od souvislostí okolo vzniku bioinformatiky sloučením informatiky a biologie tato práce uvede čtenáře do problematiky přístupu k datům týkajících se interakcí mezi proteiny. Tato práce vysvětlí důvody vzniku IMEx konsorcia, jeho cíle a prostředky, kterými svých cílů dosahuje. IMEx konsorcium dalo vzniknout mnoha standardům, které usnadňují přístup k datům členů konsorcia a výměnu těchto dat mezi nimi. Jedním z výtvorů IMEx konsorcia je i webová služba PSICQUIC, která byla navržena s využitím architektonického stylu REST, a která je přístupná i pomocí protokolu SOAP. Obě tyto kategorie přístupů k webových službám jsou v rámci této práce studovány a na základě výsledků výzkumu je implementována aplikace pro získávání interakcí mezi proteiny z databází, jenž jsou členy IMEx konsorcia.This thesis deals with different possibilities, how to collect data from bioinforatics databases containing protein interaction data. Reader is put into context by introducing him problematics of emergence of bioinformatics by connecting two fields of human knowledge: biology and informatics. Then the reader will get acquainted with the importance of protein interactions and possible ways of retrieving protein interaction data from protein interaction databases. This thesis also elucidates the motivation for IMEx consortium existence. IMEx faciliattes access to data and data exchange between its members by issuing new standards and data formats. I a list of IMEx consortium sucecsses is also PSICQUIC web service. PSICQUIC is REST-compliant web service, which can be also accessed via SOAP protocol. Both REST and SOAP approaches are studied and compared in this thesis and on the basis of this research is implemented application for retreiving protein interaction data from PSICQUIC members' databases.

Kassiopeia: A Modern, Extensible C++ Particle Tracking Package

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease of use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occuring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopei

Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care

Medical Informatics (MI) and Bioinformatics (BI) are two interdisciplinary areas located at the intersection between computer science and medicine and biology, respectively. Historically, they have been separated and only occasionally have researchers of both disciplines collaborated. The completion of the Human Genome Project has brought about in this post genomic era the need for a synergy of these two disciplines to further advance in the study of diseases by correlating essential genotypic information with expressed phenotypic information. Biomedical Informatics (BMI) is the emerging technology that aims to put these two worlds together in the new rising genomic medicine. In this regard, institutions such as the European Commission have recently launched several initiatives to support a new combined research agenda, based on the potential for synergism of both disciplines. In this paper we review the results the BIOINFOMED study one of these projects funded by the E

Internet of Things Strategic Research Roadmap

Internet of Things (IoT) is an integrated part of Future Internet including existing and evolving Internet and network developments and could be conceptually defined as a dynamic global network infrastructure with self configuring capabilities based on standard and interoperable communication protocols where physical and virtual “things” have identities, physical attributes, and virtual personalities, use intelligent interfaces, and are seamlessly integrated into the information network

Emerging technologies for learning (volume 1)

Collection of 5 articles on emerging technologies and trend

3rd EGEE User Forum

We have organized this book in a sequence of chapters, each chapter associated with an application or technical theme introduced by an overview of the contents, and a summary of the main conclusions coming from the Forum for the chapter topic. The first chapter gathers all the plenary session keynote addresses, and following this there is a sequence of chapters covering the application flavoured sessions. These are followed by chapters with the flavour of Computer Science and Grid Technology. The final chapter covers the important number of practical demonstrations and posters exhibited at the Forum. Much of the work presented has a direct link to specific areas of Science, and so we have created a Science Index, presented below. In addition, at the end of this book, we provide a complete list of the institutes and countries involved in the User Forum