Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

Abstract

Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research.

Towards a European health research and innovation cloud (HRIC)

“…It therefore seems more promising to drive standardization within research communities while looking out for opportunities for overall standardization. Thus, the workshop envisioned the HRIC as a distributed collection of data repositories, people, and services, which together make up a framework for sharing and operating as a federated data commons, with reproducible software, standards, and expertise based on joint policies and guidelines on conducting health research, much like the smaller frameworks used successfully in previous initiatives [2,[16][17][18][19]. The need for federation is also highlighted in the proposed EU action plan for 'Making sense of big data in health research' [3].…”

“…We would like to thank the scientific policy officers at the European Commission Health Directorate, who developed the workshop concept, organized it, and provided input to this publication: Sasa Jenko, Katarina Krepelkova, Christina Kyriakopoulou, Jana Makedonska, Joana Namorado, Elsa Papadopoulou, Jan Van de Loo and Gregor Schaffrath (National Expert in 17 Fondazione Toscana Life Sciences, 53100 Siena, Italy. 18 27 National Cancer Institute, Vilnius, Lithuania. 28 geneXplain GmbH, Wolfenbüttel, Germany.…”

Genomic big data hitting the storage bottleneck

“…Since several years, under the pressure of increasing volumes of data and due to reduced hardware costs, the view of databases as centralised data access points has become vaguer ( Sreenivasaiah and Kim, 2010 ). Fundamental paradigms of data organisation and storage have been revised to accommodate parallelisation, disreputability and efficiency.…”

BEW: Bioinformatics Workbench for Analysis of Biofilms Experimental Data

“…These issues were discussed with field experts -at the Eurobiofilms 2013 meeting in Ghent, Belgium (9-12 September 2013) -as means to accommodate for as much of this complexity and variability as possible, and anticipate new requirements resulting from the increasing use of high-throughput methods. Then, XML, the eXtensible Markup Language [12], was elected to formalise the data structure because of its portability and widespread acceptance as a standard data language for Bioinformatics [13].…”