Biobanking in a box (BiBBoX)

Rationale

Biobank software needs

Biological resources, such as cells, tissues or biomolecules are considered as the essential raw material frau  for the advancement of biotechnology, human health, and for research and development in life sciences. Every sample in a collection includes attached data on factors such as health status, nutrition, lifestyle, and environmental exposure. Following the rapid progress in omics-research also a wide range of high-throughput data will be attached to samples, extending the data space related to a sample collection. The handling of samples (sample management in a biobank and LIMS for downstream analysis) and related data is the main tasks of a biobanking software solution.

For the fast growing field of biobanking several commercial software solutions are upcoming, however they mostly cover only specific aspects and use proprietary data schemas, which leads to a fragmented and heterogeneous software landscape. An open-source approach can face this challenge and guarantee sustainability and data harmonisation, but most of the open-source software tools cannot be used without significant effort for installation, configuration and maintenance and lack documentation for non-IT experts.

The Solution

Open Source Software Toolbox for Biobanks

BiBBoX is an integration platform for open-source software in the bio-bank domain providing a single unified user experience. It enables bio-banks to pull together information and applications into one service where users have quick access to all services specific to their role. In a virtual machine we pre-installed, configured and connected a comprehensive set of open-source bio-bank software tools, ready to go with minimal IT effort.  The composition of the BiBBoX software toolbox will be community based, and coordinated by BBMRI.eric / BBMRI.at. 

BiBBoX is an integration platform for open-source software in the bio-bank domain providing a single unified user experience. It enables bio-banks to pull together information and applications into one service where users have quick access to all services specific to their role. In a virtual machine we pre-installed, configured and connected a comprehensive set of open-source bio-bank software tools, ready to go with minimal IT effort.  The following open source applications will be integrated:

 

BiBBoX's core database application is based on a record management (RM) system for human data and the open-source mouse house and phenotyping management system mouseDB (developed by the Helmholtz Zentrum München / Infrafrontier ) for mouse data. Using ontology tools as the DataSHaPER a bridge between different databases can be build. Such an approach will on the one hand provide a bridge between human and mouse collections and also ensure future harmonization and interoperability of biobanks

BiBBoX provides a pre-installed and configured software suite for small to medium sized application scenarios. Featured with random generated example data, interested parties can use and evaluate open-source software solutions right "out of the box".

The Foundation

Open-Source tools included in BiBBoX can be divided into the following groups:

Operating System / Foundation

  • Virtual machine (Oracle VM virtual box)
  • Portal Services,  (LifeRay)
  • Import / Export , Harvesting and Service Interfaces

Data Management

  • Sample database (Liferay record management, mouseDB)
  • Molecular database / interface to existing systems
  • Clinical database / interface to existing systems

Data Tools

  • Harmonization (e.g. DataSHaPER)
  • Classification (e.g. Patientmerger, CRIP tool)
  • Ontologies
  • Anonymization (e.g. Open Anonymizer)
  • Analysis and Visualization (e.g. glyph based visual analytics, icon library)

Integration Platform

  • Workflow Management
  • SOP support
  • Lims (e.g BIKA)
  • Trails (e.g. OpenClinica)

Besides the integration approach we developed an automatic classification system for pathological findings and multilevel data glyphs for the interactive exploration of the classified records. These tools are also included in BiBBoX and will be further develop according to the needs of the biobank community. 


Login Information

Explore the BiBBox environment in different user roles. Please note, that alle records (patients, diagnosis, samples) contain random generated information and does not relate to any real person. 

login: manager@bibbox.org
​password: bibbox2014
role: read access to all objects, anonymized access to patient information. 

login: pathologist@bibbox.org
​password: bibbox2014
role: read/write access to diganosis and patient information. 

login: scientist@bibbox.org
​password: bibbox2014
role: read access to diganosis and samples, no patient information. 

login: archivar@bibbox.org
​password: bibbox2014
role: read/write acess to sample informotion, no acesss to diagnosis and patient information