Abstract
Life sciences research in general and systems biology in particular have evolved from the simple combination of theoretical frameworks and experimental hypothesis validation to combined sciences of biology/medicine, analytical technology/chemistry, and informatics/statistics/modeling. Integrating these multiple threads of a research project at the technical and data level requires tight control and systematic workflows for data generation, data management, and data evaluation. Systems biology research emphasizes the use of multiple approaches at various molecular and functional levels, making the use of complementing technologies and the collaboration of many researchers a prerequisite. This paper presents B-Fabric, a system developed and running at the Functional Genomics Center Zurich (FGCZ), which provides a core framework for integrating different analytical technologies and data analysis tools. In addition to data capturing and management, B-Fabric emphasizes the need for quality-controlled scientific annotation of analytical data, providing the ground for integrative querying and exploitation of systems biology data. Users interact with B-Fabric through a simple Web portal making the framework flexible in terms of local infrastructure.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Brazma, A., Krestyaninova, M., Sarkans, U.: Standards for Systems Biology. Nature Reviews 7, 593–605 (2006)
Apache Cocoon, http://cocoon.apache.org/
Hack, C.J.: Integrated transcriptome and proteome data: the challenges ahead. Briefings in Functional Genomics & Proteomics 3(3), 212–219 (2004)
Apache log4j, http://logging.apache.org/log4j/docs/
Apache Lucene, http://lucene.apache.org/
Ludäscher, B., et al.: Scientific Workflow Management and the Kepler System. Concurrency and Computation: Practice and Experience 18(10) (August 2006)
Apache ObJectRelationalBridge - OJB, http://db.apache.org/ojb/
OpenJMS, http://openjms.sourceforge.net/
OpenSSH, http://www.openssh.com/
OpenSymphony - OSWorkflow, http://opensymphony.com/osworkflow/
PostgreSQL, http://www.postgresql.org/
Yu, J., Buyya, R.: A Taxonomy of Scientific Workflow Systems for Grid Computing. In: SIGMOD Record, vol. 34(3) (September 2005)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Türker, C., Stolte, E., Joho, D., Schlapbach, R. (2007). B-Fabric: A Data and Application Integration Framework for Life Sciences Research. In: Cohen-Boulakia, S., Tannen, V. (eds) Data Integration in the Life Sciences. DILS 2007. Lecture Notes in Computer Science(), vol 4544. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73255-6_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-73255-6_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73254-9
Online ISBN: 978-3-540-73255-6
eBook Packages: Computer ScienceComputer Science (R0)