Bika succeeds in bio-informatics laboratory
A master’s thesis in bio-informatics was successfully completed using leading Open Source Bika LIMS, thus far considered mainly for chemistry applications in agriculture, public health, environmental science and water quality management.
Jascha Silbermann's paper, “Information Management in the Molecular Biology Lab: Wiki and LIMS” at the Research unit for Molecular Biology and Functional Genomics at TH Wildau University of Applied Sciences, accepts that information management in a research laboratory brings together people and information, managing quality, change, diverse content and knowledge, from raw experimental data to the collective 'semantic' information within the organisation.
Complementary Free and Open Source Software (FOSS) LIMS and Wiki systems were employed to effectively deal with information across this spectrum. DokuWiki facilitated the assembly of collective laboratory knowledge, and Bika LIMS tracked RT-PCR gene expression profiling work-flow in an ISO 17025 compliant way, including samples, analyses and results.
Methods were chosen with reproducibility in mind and configured in two analysis profiles. The first, Expression Preparation, included tests for wavelength ratios 260nm/280nm and 260nm/230nm, RNA amount (μg), rRNA ratio 28s/18s, 2 different methods for RNA concentration (ng/μl) and gel electrophoresis. The second, a Gene Expression profile, measured relative expressions of six genes. Bika's file attachment feature was used to store gel electrophoresis images directly with corresponding samples.
Hardware requirements were kept at a minimum using the web-based systems from a Linux server. No disruptive modifications to user PCs were necessary. Factors considered included availability, implementation effort, effectiveness, and reproducibility of the work.
The paper discusses the findings and how to apply them to a comparable laboratory and concludes that the LIMS and Wiki combination improved the quality and availability of data and points out likely future developments, client data on hand-helds and virtual servers in the cloud, the hunt for meta-data, the description of content, and introduces a methodology for using information-intensive processes while maintaining high standards.
Researchers, in academic and commercial settings alike, are expected to publish reproducible results. It should be possible for another scientist with access to comparable hardware to repeat the experiment to review the procedure and verify results. When software is used to analyse research data, it is imperative to publish the original data as well as the exact steps which produced results as code. It is the only way to ensure reproducibility in projects involving large amounts of data and sophisticated programs. This is not possible for closed source software.
The Bika team congratulates Jascha on his achievement and wishes him a prosperous and stimulating time in his new information consultancy, and at the same time challenges him to investigate whether the Wiki part of research knowledge gathering cannot be accomplished through the content management features of Plone 4, the platform of upcoming Bika LIMS versions. If so, batching of analytical and semantic results of experiments can easily be done in the LIMS itself.
Links:
www.bikalabs.com/
consult.jascha.silbermann.name/
documents.jascha.silbermann.name/master-thesis/
Open Source laboratory information management system (LIMS) developers. Systems for ISO 17025 compliant applications in agriculture, food and beverages, environmental monitoring, bio-informatics, public health, water quality management and inter-laboratory proficiency testing.
Bika Lab Systems
Box 21721
Kloof street 8008
Cape Town
South Africa
