Periodic Reporting for period 2 - B3Africa (Bridging Biobanking and Biomedical Research across Europe and Africa)
Okres sprawozdawczy: 2017-01-01 do 2018-09-30
A warmer climate means that global production systems will change and in an increasingly globalised world both opportunities and diseases spreads more quickly than before. The recent Ebola outbreaks have here served as a major alarm clock highlighting the needs for a combination of global collaboration and strong local infrastructures for both research and treatment.
The B3Africa project has engaged in capacity building to support equitable collaboration between researchers in low, middle and high income countries. Historically sample collection in low income countries has been followed by them being exported to wealthier partners with little benefit to local communities. This is neither acceptable nor an efficient usage of resources as locally placed researchers are far better positioned to exploit results and conduct follow up studies. By creating an informatics platform that enables researchers to not only collect samples, but to generate data and analyse it B3Africa project has contributed to more sustainable and equitable research.
The overall objective of the project has been to create a technical and intellectual platform integrating the necessary training, collaboration framework and available open source software to be used by African and European biobanks and research institutions. Researchers can thereby create a functioning biobank out of the box with the eB3Kit or use the modular system to improve established research operations. High quality research can thereby be established in a global context at a low cost, creating more efficient supply chains for providing biospecimen suited for high-throughput experiments and longitudinal studies.
The B3Africa project has engaged in capacity building to support equitable collaboration between researchers in low, middle and high income countries. Historically sample collection in low income countries has been followed by them being exported to wealthier partners with little benefit to local communities. This is neither acceptable nor an efficient usage of resources as locally placed researchers are far better positioned to exploit results and conduct follow up studies. By creating an informatics platform that enables researchers to not only collect samples, but to generate data and analyse it B3Africa project has contributed to more sustainable and equitable research.
The overall objective of the project has been to create a technical and intellectual platform integrating the necessary training, collaboration framework and available open source software to be used by African and European biobanks and research institutions. Researchers can thereby create a functioning biobank out of the box with the eB3Kit or use the modular system to improve established research operations. High quality research can thereby be established in a global context at a low cost, creating more efficient supply chains for providing biospecimen suited for high-throughput experiments and longitudinal studies.
BBIOETHICS, LAW AND COLLABORATION
For collaboration an Ethical and Legal Framework was built on a dual approach; first, collaborative efforts have been made to identify minimum threshold principles that all users of the eB3Kit should abide by. Secondly, solutions for conflict of laws are to be used in individual cases; based on legal possibilities and avenues for the transfer of data.
The minimum threshold principles established within the first approach were implemented in the B3Africa platform in the form of a Model Data Management Policy (MDMP). Using MDMP it becomes easier for researchers to negotiate and conduct responsible sharing between the EU and states in Africa or collaborations with the industry.
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.
EDUCATION & TRAINING
Monitoring and evaluation of learning events was an integrated part of the B3Africa Training Plan. Towards the end of the reporting period, an outcome analysis of the main learning events was performed.
The first learning events organized addressed prerequisite knowledge and skills. Tool-specific competencies were planned to be addressed in a later stage, since the platform and tools had first to be developed by other work packages. 59% of the webinar attendees were professionals based in Africa (37% from Europe and 4% from elsewhere). The frequency of attendance was also higher in Africa, with 75% of the professionals who attended more than 3 webinars based in this region. This suggested that the technology used for this type of training event was rather an incentive than an obstacle to learning in Africa.
Learning material produced by IARC, in collaboration with other partners include documentation for software components and:
*The eight B3Africa webinars were recorded. Video recordings were cut into thematic sequences and edited in a harmonized way, to produce a total of 17 educational video-based modules that may be watched by any professional interested in the topic. Modules include video recording of webinars, a PDF copy of the PowerPoint presentation, and quiz and exercises when relevant.
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*(7) lectures giving during the B3Africa second in-person training and dissemination workshop were also recorded for consultation by biobank and research professionals.
INTEGRATION OF SOFTWARE
The main software solutions created by the project are: Baobab Laboratory Information Management System (Baobab LIMS), the Galaksio interface for Galaxy, Azizi data collection tool and the integration platform BIBBOX. The eB3Kit is an instance of the BIBBOX that can be deployed in a physical computer or a virtual server. A mobile platform for use in field work applications has also been developed and showcased.
Software components of B3Africa project are provided as Docker containers (a light weight operating-system-level virtualization) through the BIBBOX app store. A BIBBOX Demo server is hosted by the Medical University of Graz (WP2; integration) and a BIBBOX is also hosted at ILRI, Nairobi:
http://demo.bibbox.org/
http://bibbox.azizi.ilri.org
The source code for BIBBOX and repositories for the BIBBOX applications are available on Github:
https://github.com/bibbox
Tools developed by B3Africa are also available as standalone open source software.
The Galaksio interface for Galaxy is available as a Docker container and as a Github repository:
https://hub.docker.com/r/tklingstrom/galaksio/
https://github.com/SGBC/galaksio
Azizi data collection Github repository
https://github.com/bibbox/app-azizi-onadata
Baobab LIMS is available for download from Github or the SANBI website:
Download:
*https://github.com/hocinebendou/baobab.lims.git
*http://christoffels.sanbi.ac.za/index.php/software/software-downloads
A fully functional demo is available at:
*http://b3abiobank.sanbi.ac.za/demo (login=admin; password=admin)
For collaboration an Ethical and Legal Framework was built on a dual approach; first, collaborative efforts have been made to identify minimum threshold principles that all users of the eB3Kit should abide by. Secondly, solutions for conflict of laws are to be used in individual cases; based on legal possibilities and avenues for the transfer of data.
The minimum threshold principles established within the first approach were implemented in the B3Africa platform in the form of a Model Data Management Policy (MDMP). Using MDMP it becomes easier for researchers to negotiate and conduct responsible sharing between the EU and states in Africa or collaborations with the industry.
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.
EDUCATION & TRAINING
Monitoring and evaluation of learning events was an integrated part of the B3Africa Training Plan. Towards the end of the reporting period, an outcome analysis of the main learning events was performed.
The first learning events organized addressed prerequisite knowledge and skills. Tool-specific competencies were planned to be addressed in a later stage, since the platform and tools had first to be developed by other work packages. 59% of the webinar attendees were professionals based in Africa (37% from Europe and 4% from elsewhere). The frequency of attendance was also higher in Africa, with 75% of the professionals who attended more than 3 webinars based in this region. This suggested that the technology used for this type of training event was rather an incentive than an obstacle to learning in Africa.
Learning material produced by IARC, in collaboration with other partners include documentation for software components and:
*The eight B3Africa webinars were recorded. Video recordings were cut into thematic sequences and edited in a harmonized way, to produce a total of 17 educational video-based modules that may be watched by any professional interested in the topic. Modules include video recording of webinars, a PDF copy of the PowerPoint presentation, and quiz and exercises when relevant.
even
*(7) lectures giving during the B3Africa second in-person training and dissemination workshop were also recorded for consultation by biobank and research professionals.
INTEGRATION OF SOFTWARE
The main software solutions created by the project are: Baobab Laboratory Information Management System (Baobab LIMS), the Galaksio interface for Galaxy, Azizi data collection tool and the integration platform BIBBOX. The eB3Kit is an instance of the BIBBOX that can be deployed in a physical computer or a virtual server. A mobile platform for use in field work applications has also been developed and showcased.
Software components of B3Africa project are provided as Docker containers (a light weight operating-system-level virtualization) through the BIBBOX app store. A BIBBOX Demo server is hosted by the Medical University of Graz (WP2; integration) and a BIBBOX is also hosted at ILRI, Nairobi:
http://demo.bibbox.org/
http://bibbox.azizi.ilri.org
The source code for BIBBOX and repositories for the BIBBOX applications are available on Github:
https://github.com/bibbox
Tools developed by B3Africa are also available as standalone open source software.
The Galaksio interface for Galaxy is available as a Docker container and as a Github repository:
https://hub.docker.com/r/tklingstrom/galaksio/
https://github.com/SGBC/galaksio
Azizi data collection Github repository
https://github.com/bibbox/app-azizi-onadata
Baobab LIMS is available for download from Github or the SANBI website:
Download:
*https://github.com/hocinebendou/baobab.lims.git
*http://christoffels.sanbi.ac.za/index.php/software/software-downloads
A fully functional demo is available at:
*http://b3abiobank.sanbi.ac.za/demo (login=admin; password=admin)
The B3Africa project has made significant contributions towards the establishment of a more fine-grained network of research institutions capable of carrying out high quality omics-research in low- or middle-income countries (LMICs). Without engaged local stakeholders, research quickly degenerate into a patchwork of findings but with little potential for follow ups or incentives for long term capacity building. The B3Africa project has helped to alleviate these issues by combining capacity building with a technical platform which can reduce the costs to establish high quality biobank-based research in LMICs.
The B3Africa project has played an important role to bridge Biobanking and Biomedical Research across Europe and Africa by helping to establish an ethical, legal and technical foundation for equal collaboration between researchers. The technical implementations made by the project significantly reduces the costs and complexity of establishing high quality sample collections in resource constrained settings, while training and legal frameworks ensures that successful and equal partnerships between researchers from many nations can more easily be established. The eB3Kit implementation also provides researchers with a highly portable informatics platform which can be combined with portable machines such as the Oxford Nanopore or field kits for point of care diagnostics, thus enabling researchers and epidemiologists with the necessary equipment to quickly establish a mobile or semi-mobile field laboratory. Such laboratories can serve an important role for data collection in basic research as well as a powerful tool to deal with disease outbreaks and other emerging threats.
The B3Africa project has played an important role to bridge Biobanking and Biomedical Research across Europe and Africa by helping to establish an ethical, legal and technical foundation for equal collaboration between researchers. The technical implementations made by the project significantly reduces the costs and complexity of establishing high quality sample collections in resource constrained settings, while training and legal frameworks ensures that successful and equal partnerships between researchers from many nations can more easily be established. The eB3Kit implementation also provides researchers with a highly portable informatics platform which can be combined with portable machines such as the Oxford Nanopore or field kits for point of care diagnostics, thus enabling researchers and epidemiologists with the necessary equipment to quickly establish a mobile or semi-mobile field laboratory. Such laboratories can serve an important role for data collection in basic research as well as a powerful tool to deal with disease outbreaks and other emerging threats.