openBEB: open biological experiment browser for correlative measurements

Abstract

BackgroundNew 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.ResultsWe 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.ConclusionsThe 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.

Influence of squeeze-film damping on higher-mode microcantilever vibrations in liquid

“…A Zurich Instruments HF2 lock-in amplifier was employed to record cantilever resonance spectra by sweeping a given range of excitation frequencies and demodulating the corresponding phase and amplitude (lock-in bandwidth = 4.38 Hz, filter order = 24 dB/octave, 1000 data points). The setup was controlled using LabVIEW (National Instruments) and measurements were automated using the openBEB macro language [23]. The automation involved acquisition of spectra, adjusting the cantilever-surface gap, and adjusting the laser power and position of the laser spot on the positionsensitive detector using a proportional-integral-derivative (PID) controller.…”

qPortal: A platform for data-driven biomedical research

“…Access rights are managed on the top level (workspaces), which can contain multiple projects, experiments, samples and datasets. Custom openBIS data models can be defined by creating specific types for experiments, samples and datasets and standard plugins for common biomedical experiment types are already available [ 23 ]. Entities of those types can contain multiple user-defined properties.…”

Array based real-time measurement of fluid viscosities and mass-densities to monitor biological filament formation

“…The new control software was developed as an openBEB module 32 in LabVIEW. To collect and save the amplitude and phase data, a separate module was programmed, which enables the user to perform either a single sweep or a sequential acquisition of a specific frequency range.…”