Community Research and Development Information Service - CORDIS

H2020

B3Africa Report Summary

Project ID: 654404
Funded under: H2020-EU.1.4.3.2.

Periodic Reporting for period 1 - B3Africa (Bridging Biobanking and Biomedical Research across Europe and Africa)

Reporting period: 2015-07-01 to 2016-12-31

Summary of the context and overall objectives of the project

There is lack of a standardised platform that manage Biobanks and Biorepositories across Europe and Africa and platforms for conducting Bioinformatics analysis. This, coupled with the disparity of research institutions (in terms of human capacity and infrastructure) in Europe and in Africa, creates a disharmony in how research is conducted in Europe and Africa. It also affects the level of collaborations between researchers in the 2 continents. The B3Kit aims at providing researchers with a standardised platform to manage biobanks and biorepositories and to conduct bioinformatics teaching and research.

The problems affecting humanity have become globalised and are no longer confined to regions or countries or continents. The recent Ebola crisis has shown us that there is need for a globalised coordinated approach towards solving problems that affect humanity and this calls upon standardising the way research is conducted across the globe. The eB3Kit attempts at providing a standard platform for research across the EU and Africa.

The overall objective of the project is to create a technical and intellectual platform, that can bridge European and African biobanking and research, by integrating available open source software, services and tools as well as public databases to be used in African and European biobanks and research institutions.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

"BIOETHICS

B3Africa delineated a "Model Data Management Policy" for personal data protection and data sharing and integration.
The modelling personal data protection for sharing biobank and bio-molecular data was designed based on MIABIS 2.0, the de facto standard for BBMRI-ERIC; and it is also based on the specified rules from B3Africa`s Ethical framework document.

This model, together with the data management policy is used by WP2 (integration), WP3 (biobanking), WP4 (bioinformatics) to design the proof of concept of this project, WP7 (use case) to demonstrate biobanking interoperability, bioinformatics and education and training.

BIOBANKING LIMS

The primary work by B3Africa was to develop an open source laboratory information management system (LIMS). This LIMS will be provided as a component to the biobank in a box (BiBBox platform).

The collaboration of B3Africa work packages together with developers at Bika Labs, identified the key modules needed for a LIMS to function in a human biobank setting.

Through a series of initial joint brainstorming sessions between partners B3Africa refined the specification needed for developing the LIMS hereafter known as Baobab LIMS.
The NSB Biobank based at the University of Stellenbosch, Cape Town provided the use case for developing laboratory workflows that are integral to the biobank services at NSB.

The following tasks were identified at the start of the project and delivered:
(a) Kit assembly and Distribution module
(b) Shipping module
(c) Sample storage and inventory
(d) Access Policy
(e) Freezer management
(f) Invoicing

Through a process of code development and testing at NSB B3Africa developed Baobab LIMS with the following functionality:
(a) A client project is registered in the LIMS
(b) Project-specific information is captured at the appropriate laboratory biospecimen kits are assembled
(c) Biospecimen kits are shipped to the client and returned with the specific biospecimen (DNA or RNA) for storage and analysis
(d) A freezer management module has been developed to specific the location of each biospecimen or sample.
(e) Interfaces for two analytical tools (Qubit fluoromter and Biodrop uLite.) were developed by a MSc student

The completion of version 1.0 of the B3aobab provides researchers with a laboratory management system (LIMS) where biospecimens can be tracked in a lab. The software is open source and allows any research lab to customise this software for their own needs.

Another relevant component related to biobanking, is the data collection in the field software developed by ILRI: ODK. This system allows the collection and updating of data using a mobile device. During the 3rd Jamboree in Graz, the integration of the ODK with one sample management system provided as part of the BiBBox (OpenSpecimen), was tested.

BIOINFORMATICS
Work on the bioinformatics platform part of the eB3Kit is progressing as planned. B3Africa has produced Galaksio; a simplified user interface for bioinformatics workflow management.
This product can be downloaded as a docker image from Github along with an iRods-Galaxy integrator written in Python.
To support integration of pre-analytical data into the analysis pipelines, it was decided to use the "Stategra Experimental Management System" developed by the STATegra project (EU FP7 grant number 30600).
This management system will be integration point between sample management and bioinformatics in the eB3Kit along with the previously selected software.
One priority of B3Africa is to package tools and create analysis workflows that will be accessed through the Galaksio interface.

INTEGRATION

All the software components of B3Africa project are provided as Docker containers (Virtual machine environment) through the BiBBox platform.
Some interfaces between application are being implemented and tested to create workflows between applications that guarantee the provenance and flow of data from the biobank to the bioinformatics analysis and vice versa.

A BiBBox Demo server is hosted by the Medical University of Graz (WP2; integration):
http://demo.bibbox.org/

All tools developed by B3Africa can be downloaded and used as open source software.

https://hub.docker.com/r/fikipollo/galaksio/
https://github.com/fikipollo/stategraems
https://github.com/fikipollo/iRODS-in-Galaxy

Baobab LIMS is available as follows:
Download:
https://github.com/hocinebendou/baobab.lims.git
http://christoffels.sanbi.ac.za/index.php/software/software-downloads
Demo:
login=admin; password=admin

So far, the main software solutions created by the project are: B3aobab LIMS, Galaksio and the integration platform BiBBox. One eB3Kit is an instance of the BiBBox that can be deployed in a physical computer or a virtual server."

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The expected impacts of B3Africa project provided in the DoA are:
• Develop cooperation with key international partners for research infrastructures
• Contribute to the development of a competitive high performance ERA in the global research environment
• Enhance the role of the Union in international organisations and multilateral fora
• Reducing the threat of diseases spreading as a result of global warming
• Contribute to capacity building and research infrastructures human capital development in targeted/relevant regions
Those expected impacts are still valid and we are working towards the fully achievement of them.

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