B-Fabric: A Data and Application Integration Framework for Life Sciences Research

Türker, Can; Stolte, Etzard; Joho, Dieter; Schlapbach, Ralph

doi:10.1007/978-3-540-73255-6_6

Cited by 11 publications

(7 citation statements)

References 4 publications

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“…Direct tool access is beyond the current scope of B-Fabric. Accordingly, it provides no such facilities [5].…”

Section: Related Workmentioning

confidence: 99%

“…We have developed a web service for accessing diverse statistical analysis methods. A similar solution was explored inside the Bioconductor project 5 where an R package, namely RWebServices, was developed. The RWebServices approach is to convert R functions to Java objects and methods for exposure as Java-based web services [8].…”

Section: Related Workmentioning

confidence: 99%

“…Data management in the life sciences has been a very active area of research for a number of years ( [2], [3], [4], [5]). Over time, it has become obvious, that it does not suffice for tools to offer "just" integrated (centralized or virtual) data storage capabilities.…”

Section: Introductionmentioning

confidence: 99%

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A flexible statistics web processing service - Added value for information systems for experiment data

Heimann

Nieschulze

König‐Ries

2010

Journal of Integrative Bioinformatics

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SummaryData management in the life sciences has evolved from simple storage of data to complex information systems providing additional functionalities like analysis and visualization capabilities, demanding the integration of statistical tools. In many cases the used statistical tools are hard-coded within the system. That leads to an expensive integration, substitution, or extension of tools because all changes have to be done in program code. Other systems are using generic solutions for tool integration but adapting them to another system is mostly rather extensive work. This paper shows a way to provide statistical functionality over a statistics web service, which can be easily integrated in any information system and set up using XML configuration files. The statistical functionality is extendable by simply adding the description of a new application to a configuration file. The service architecture as well as the data exchange process between client and service and the adding of analysis applications to the underlying service provider are described. Furthermore a practical example demonstrates the functionality of the service.

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“…Direct tool access is beyond the current scope of B-Fabric. Accordingly, it provides no such facilities [5].…”

Section: Related Workmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

See 1 more Smart Citation

A flexible statistics web processing service - Added value for information systems for experiment data

Heimann

Nieschulze

König‐Ries

2010

Journal of Integrative Bioinformatics

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“…There exist several integrated systems for proteomics data management, examples are PRISM [5] or B-Fabric [6]. These systems are usually designed for the business use cases of specific research facilities.…”

Section: Introductionmentioning

confidence: 99%

FCC – An automated rule-based processing tool for life science data

Barkow-Oesterreicher

Türker

Panse

2013

Source Code Biol Med

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BackgroundData processing in the bioinformatics field often involves the handling of diverse software programs in one workflow. The field is lacking a set of standards for file formats so that files have to be processed in different ways in order to make them compatible to different analysis programs. The problem is that mass spectrometry vendors at most provide only closed-source Windows libraries to programmatically access their proprietary binary formats. This prohibits the creation of an efficient and unified tool that fits all processing needs of the users. Therefore, researchers are spending a significant amount of time using GUI-based conversion and processing programs. Besides the time needed for manual usage, such programs also can show long running times for processing, because most of them make use of only a single CPU. In particular, algorithms to enhance data quality, e.g. peak picking or deconvolution of spectra, add waiting time for the users.ResultsTo automate these processing tasks and let them run continuously without user interaction, we developed the FGCZ Converter Control (FCC) at the Functional Genomics Center Zurich (FGCZ) core facility. The FCC is a rule-based system for automated file processing that reduces the operation of diverse programs to a single configuration task. Using filtering rules for raw data files, the parameters for all tasks can be custom-tailored to the needs of every single researcher and processing can run automatically and efficiently on any number of servers in parallel using all available CPU resources.ConclusionsFCC has been used intensively at FGCZ for processing more than hundred thousand mass spectrometry raw files so far. Since we know that many other research facilities have similar problems, we would like to report on our tool and the accompanying ideas for an efficient set-up for potential reuse.

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“…Without an integrated data management solution these tasks are hardly to accomplish. Consequently, we have developed B-Fabric [1], a web-based data management system for supporting life sciences projects and integrating the produced data and needed applications.…”

Section: Introductionmentioning

confidence: 99%

Life Sciences Data and Application Integration with B-Fabric

Türker

Akal

Schlapbach

2011

Journal of Integrative Bioinformatics

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In this demo paper, we sketch B-Fabric, an all-in-one solution for management of life sciences data. B-Fabric has two major purposes. First, it is a system for the integrated management of experimental data and scientific annotations. Second, it is a system infrastructure supporting on-the fly coupling of user applications, and thus serving as extensible platform for fast-paced, cutting-edge, collaborative research. SummaryIn this demo paper, we sketch B-Fabric, an all-in-one solution for management of life sciences data. B-Fabric has two major purposes. First, it is a system for the integrated management of experimental data and scientific annotations. Second, it is a system infrastructure supporting on-the fly coupling of user applications, and thus serving as extensible platform for fast-paced, cutting-edge, collaborative research.

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B-Fabric: A Data and Application Integration Framework for Life Sciences Research

Cited by 11 publications

References 4 publications

A flexible statistics web processing service - Added value for information systems for experiment data

A flexible statistics web processing service - Added value for information systems for experiment data

FCC – An automated rule-based processing tool for life science data

Life Sciences Data and Application Integration with B-Fabric

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