From the evaluation of existing solutions to an all-inclusive package for biobanks

BIBBOX, a FAIR toolbox and App Store for life science research

Data quality has recently become a critical topic for the research community. European guidelines recommend that scientific data should be made FAIR: findable, accessible, interoperable and reusable. However, as FAIR guidelines do not specify how the stated principles should be implemented, it might not be straightforward for researchers to know how actually to make their data FAIR. This can prevent life-science researchers from sharing their datasets and pipelines, ultimately hindering the progress of research. To address this difficulty, we developed the BIBBOX, which is a platform that supports researchers publishing their datasets and the associated software in a FAIR manner.

Setting the Foundations: Individual Rights, Public Interest, Scientific Research and Biobanking

The principle of conferral tames the EU competence to regulate research in a comprehensive manner, yet furthering research is one of its aspirations. Data protection, however, is an area within which the EU has legislated extensively. During the development of the General Data Protection Regulation (GDPR), an important issue to tackle was how to balance the ambitious EU aspirations and differing stakeholder interests, on the one hand, with limited competences in research regulation, on the other, and how to determine the extent to which data protection could be used as a means to further scientific research in the EU legal order. The outcome is the GDPR multifaceted research regime that sets forth EU policy and opens up for further regulations from the Member States as well as the EU.

The research regime that the GDPR has created poses numerous questions. Key among these is, what are the implications of the operationalisation of Article 89 GDPR in biobanking? This chapter sets out some of the underlying tensions in the area and pins down key conceptual foundations for the book. It provides insights into the EU’s interests in the area of biobanking and maps out central elements of the research regime that has been built within the GDPR. Thereafter, it analyses the key concepts used in the book, including biobank and biobanking, scientific research as undertaken under the GDPR, individual rights and public interest. Lastly, it shares some preliminary reflections as starting points for the analysis to come.

LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata

Background

Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data generated locally by vendor software.

Results

To address this problem, we created LabPipe, a flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study.

Conclusions

LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.

The RNA workbench 2.0: next generation RNA data analysis

RNA has become one of the major research topics in molecular biology. As a central player in key processes regulating gene expression, RNA is in the focus of many efforts to decipher the pathways that govern the transition of genetic information to a fully functional cell. As more and more researchers join this endeavour, there is a rapidly growing demand for comprehensive collections of tools that cover the diverse layers of RNA-related research. However, increasing amounts of data, from diverse types of experiments, addressing different aspects of biological questions need to be consolidated and integrated into a single framework. Only then is it possible to connect findings from e.g. RNA-Seq experiments and methods for e.g. target predictions. To address these needs, we present the RNA Workbench 2.0 , an updated online resource for RNA related analysis. With the RNA Workbench we created a comprehensive set of analysis tools and workflows that enables researchers to analyze their data without the need for sophisticated command-line skills. This update takes the established framework to the next level, providing not only a containerized infrastructure for analysis, but also a ready-to-use platform for hands-on training, analysis, data exploration, and visualization. The new framework is available at https://rna.usegalaxy.eu , and login is free and open to all users. The containerized version can be found at https://github.com/bgruening/galaxy-rna-workbench.

From engaging publics to engaging knowledges: Enacting "appropriateness" in the Austrian biobank infrastructure

While there is consensus on the essential importance of public engagement in further developments of biobanking, the related investigation of public views predominantly focused on the concerns expressed by the publics, and the concrete formats of public engagement, without delving into the ways these concerns are constituted. In this article, we summarize recent research on public engagement in order to describe the constitution of respective concerns as "engagement of knowledges." By shifting the focus of analysis from "publics" to "knowledges," we draw attention to the interaction dynamic through which citizens embed the new knowledge they receive during expert interactions into the stock of knowledge they already possess. Analyzing our recent investigation of public views on biobanking in the form of citizen-expert panels in the Austrian infrastructure of biobanks (BBMRI.at), we trace this dynamic through citizens' recurrent concerns that the research and consent practices related to biobanking should be "appropriate."

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software (www.bikalims.org) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server–client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.