Brunn: An open source laboratory information system for microplates with a graphical plate layout design process

Jonathan Alvarsson,Rolf Larsson,Claes Andersson,Jarl Es Wikberg,Ola Spjuth

doi:10.1186/1471-2105-12-179

Jonathan Alvarsson, Rolf Larsson + Show 3 more

Open Access

https://doi.org/10.1186/1471-2105-12-179

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Abstract

BackgroundCompound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open system for handling plate design, and validation and preparation of data.ResultsA Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves.ConclusionsBrunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC50 values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.

Highlights

Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays
Modeling wet-laboratory experiments in a computerized information system is a non-trivial task and needs a flexible system capable of supporting the daily laborative work related to microplates, which are the main media used in high-throughput assay systems
The system is designed to help in refining raw data and encourages re-use of layouts for the plates, Brunn focuses on providing a platform for fluctuating plate layouts; here we demonstrate it on a fluorometric microculture cytotoxicity assay (FMCA) in use at the university hospital of Uppsala, Sweden

Summary

Introduction

Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. The outer dimension of microplates is standardized, but the plates are available with different numbers of wells and volumes. Microplates can be handled both manually and by robots, and they facilitate sample handling and serial dilutions by transferring solutions across rows or columns in parallel. They can be manufactured with different optical properties, such as for fluorescent read-outs, colorimetric assays, and microscopy. Microplates are available in a variety of standardized densities, where 8 rows × 12 columns = 96 wells with a volume of 200-300 μL are the most suited to be handled manually. Plates with higher densities than this are difficult to use; one reason for this is that the small volumes of liquid in each well evaporate quite fast

Results

Discussion

Conclusion