Limits...
openBEB: open biological experiment browser for correlative measurements.

Ramakrishnan C, Bieri A, Sauter N, Roizard S, Ringler P, Müller SA, Goldie KN, Enimanev K, Stahlberg H, Rinn B, Braun T - BMC Bioinformatics (2014)

Bottom Line: To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches.The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program.In this example, measurements from diverse complementary techniques are combined and correlated.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, Universität Basel, Basel, Switzerland. Thomas.Braun@unibas.ch.

ABSTRACT

Background: New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis.

Results: We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository.

Conclusions: The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated.

Show MeSH
Communication diagram explaining and illustrating the uploading of an openBEB bundle to openBIS [[6]].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3987129&req=5

Figure 14: Communication diagram explaining and illustrating the uploading of an openBEB bundle to openBIS [[6]].

Mentions: The data synchronization plug-in for openBIS is a standard plug-in supplied with openBEB (Figure 14). The openBIS data synchronization plug-in stores the raw-data and the accompanying metadata in openBIS. Just pushing the data to the server is not sufficient; information about the experiment that produced the data and the biological and technical samples that were measured is required as well. To reinforce this connection, the openBEB synchronization process creates an experiment and sample in openBIS. Information about the experiment and sample are important for data-provenance tracking.


openBEB: open biological experiment browser for correlative measurements.

Ramakrishnan C, Bieri A, Sauter N, Roizard S, Ringler P, Müller SA, Goldie KN, Enimanev K, Stahlberg H, Rinn B, Braun T - BMC Bioinformatics (2014)

Communication diagram explaining and illustrating the uploading of an openBEB bundle to openBIS [[6]].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3987129&req=5

Figure 14: Communication diagram explaining and illustrating the uploading of an openBEB bundle to openBIS [[6]].
Mentions: The data synchronization plug-in for openBIS is a standard plug-in supplied with openBEB (Figure 14). The openBIS data synchronization plug-in stores the raw-data and the accompanying metadata in openBIS. Just pushing the data to the server is not sufficient; information about the experiment that produced the data and the biological and technical samples that were measured is required as well. To reinforce this connection, the openBEB synchronization process creates an experiment and sample in openBIS. Information about the experiment and sample are important for data-provenance tracking.

Bottom Line: To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches.The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program.In this example, measurements from diverse complementary techniques are combined and correlated.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, Universität Basel, Basel, Switzerland. Thomas.Braun@unibas.ch.

ABSTRACT

Background: New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis.

Results: We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository.

Conclusions: The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated.

Show MeSH