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.

cql - A Flat File Database Query Language

cql is a UNIX system tool that applies C style query expressions to flat file databases. In some respects it is yet another addition to the toolbox of programmable file filters: grep [Hume88], sh [Bour78][BK89], awk [AKW88], and perl [Wall]. However, by restricting its problem domain, cql takes advantage of optimizations not available to these more general purpose tools. This paper describes the cql data description and query language, query optimizations, and provides comparisons with other tools. 1 Introduction Flat file databases are common in UNIX system environments. They consist of newline terminated records with a single character that delimits fields within each record. Well known examples are /etc/passwd and /etc/group, and more recently the sablime [CF88] MR databases and cia [Chen89] abstraction databases. There are two basic flat file database operations: update -- delete, add or modify records query -- scan for records based on field selection function For the most..

The Sea of Stuff: a model to manage shared mutable data in a distributed environment

Managing data is one of the main challenges in distributed systems and computer science in general. Data is created, shared, and managed across heterogeneous distributed systems of users, services, applications, and devices without a clear and comprehensive data model. This technological fragmentation and lack of a common data model result in a poor understanding of what data is, how it evolves over time, how it should be managed in a distributed system, and how it should be protected and shared. From a user perspective, for example, backing up data over multiple devices is a hard and error-prone process, or synchronising data with a cloud storage service can result in conflicts and unpredictable behaviours. This thesis identifies three challenges in data management: (1) how to extend the current data abstractions so that content, for example, is accessible irrespective of its location, versionable, and easy to distribute; (2) how to enable transparent data storage relative to locations, users, applications, and services; and (3) how to allow data owners to protect data against malicious users and automatically control content over a distributed system. These challenges are studied in detail in relation to the current state of the art and addressed throughout the rest of the thesis. The artefact of this work is the Sea of Stuff (SOS), a generic data model of immutable self-describing location-independent entities that allow the construction of a distributed system where data is accessible and organised irrespective of its location, easy to protect, and can be automatically managed according to a set of user-defined rules. The evaluation of this thesis demonstrates the viability of the SOS model for managing data in a distributed system and using user-defined rules to automatically manage data across multiple nodes."This work was supported by Adobe Systems, Inc. and EPSRC [grant number EP/M506631/1]" - from the Acknowledgements pag