Supporting multiple isolation levels in replicated environments

Replication is used by databases to implement reliability and provide scalability. However, achieving transparent replication is not an easy task. A replicated database is transparent if it can seamlessly replace a standard stand-alone database without requiring any changes to the components of the system. Database replication transparency can be achieved if: (a) replication protocols remain hidden for all other components of the system; and (b) the functionality of a stand-alone database is provided. The ability to simultaneously execute transactions under different isolation levels is a functionality offered by all stand-alone databases but not by their replicated counterparts. Allowing different isolation levels may improve overall system performance. For example, the TPC-C benchmark specification tolerates execution of some transactions at weaker isolation levels in order to increase throughput of committed transactions. In this paper, we show how replication protocols can be extended to enable transactions to be executed under different isolation levels. © 2012 Elsevier B.V. All rights reserved.This work has been supported by the Spanish Ministerio de Ciencia e Innovation (MICINN) and the European Regional Development Fund (ERDF/FEDER) under research grants TIN2009-14460-C03-01 and TIN2010-17193. The translation of this paper was funded by the Universitat Politecnica de Valencia, Spain.Bernabe Gisbert, JM.; Muñoz Escoí, FD. (2012). Supporting multiple isolation levels in replicated environments. Data and Knowledge Engineering. 79-80:1-16. doi:10.1016/j.datak.2012.05.001S11679-8

AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se

Multiple Buffer Pools and Dynamic Resizing of Buffer Pools

An autonomic database management system is a self tuning, self optimizing, self healing and self protecting database management system (DBMS). Since expert database administrators (DBAs) are scarce, introducing a DBMS that is self tuning will decrease the total cost of ownership of the system. In this thesis we present a first step to incorporating self tuning capabilities in the PostgreSQL DBMS. The buffer area is the main memory management area of the DBMS. Effective use of this area ensures efficiency of the DBMS. Some DBMSs split the buffer area into multiple buffer pools and this has led to performance increases in some cases. Once multiple buffer pools are supported it is up to the DBA to size them based on each of their needs. Optimal sizing leads to good performance, therefore, as the workload changes the DBA has to adjust the sizes of the buffer pools. We extend PostgreSQL (Version 7.3.2) to support multiple buffer pools. We remove the dependency on the DBA and automatically adjust the sizes of the buffer pools to changes in the environment. We present a number of experiments to verify our approach