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Open Access Highly Accessed Software

openBEB: open biological experiment browser for correlative measurements

Chandrasekhar Ramakrishnan23, Andrej Bieri1, Nora Sauter1, Sophie Roizard4, Philippe Ringler1, Shirley A Müller1, Kenneth N Goldie1, Kaloyan Enimanev2, Henning Stahlberg1, Bernd Rinn23 and Thomas Braun1*

Author Affiliations

1 Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, Universität Basel, Basel, Switzerland

2 Center for Information Sciences and Databases (C-ISD), Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland

3 Swiss Institute of Bioinformatics, Biozentrum, Universität Basel, Basel, Switzerland

4 Laboratory of Physical Chemistry of Polymers and Membranes (LCPPM), École Polytechnique Federale de Lausanne, Lausanne, Switzerland

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BMC Bioinformatics 2014, 15:84  doi:10.1186/1471-2105-15-84

Published: 26 March 2014

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.