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Message from the Project Coordinator
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Pending text from Erik
By Erik Bongcam-Rudloff
Swedish University of Agricultural Sciences, Sweden
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Dissemination Activities: Highlights
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B3Africa booth and award-winning poster at the Europe Biobank Week, Austria, September 2018.
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In this final edition of the newsletter, it is a pleasure to share with you highlights of the dissemination work package (WP) and events that were undertaken by the B3Africa project. The activities were designed to target researchers, IT and ethics personnel and policy makers contacted through project specific events, workshops and international conferences, focusing on biobanking, biosecurity and research. We were successful in covering a range of interests from emerging infectious diseases to non-communicable diseases and cancer, dealing with all aspects of sample and data sharing from ethical and legal frameworks to quality management. Read more.
By Maimuna Mendy
International Agency for Research on Cancer
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The "Use Case" Work Package: A Proof of Concept
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The main aim of the B3Africa "Use Case" work package (WP 7) was to implement the B3Africa informatics platform (eB3Kit) in several use case institutions as proof-of-concept. The most relevant achievements were planned and executed in synergy with WP 5 (Education and Training). The eB3Kit was installed and tested in all the use case institutions. Besides, the most relevant component of the platform, the Baobab LIMS developed by WP 3, has raised a lot of interest from biomedical research institutions in Africa and Europe. The BIBBOX developed by WP 2 is the operating system for the eB3Kit. Its concept has evolved from an "apps" store for LifeScience to a complete suit for managing and integrating open source software and generated data. It can use virtualization or can function as a physical portable box that provides a mini cluster for processing and storing data, and a network to connect several users. Read more.
By Roxana Merino Martinez
Karolinska Institutet, Sweden
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Image 1: Pilot implementation of the informatics platform at the Medical Research Council Gambia (MRCG at LSHTM), September 2018. Images 2 and 3: Representatives from the Use Case work package presenting the eB3Kit to different stakeholders at the Global Biobank Week, Sweden, September 2017.
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Baobab LIMS: Gaining Interest Beyond the Project
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Baobab LIMS has been gaining interest from a variety of laboratories and institutions. Various sites have been testing and implementing their workflows in Baobab LIMS and user feedback has provided the team with valuable information for enhancements such as the addition of modules for batch sample recording. Further additional modules allowing for the capture of data related to the patient, disease ontology and anatomical site terms, has made Baobab LIMS MIABIS compliant. In addition, the Baobab LIMS developers have finalized APIs allowing for data federation and integration. Baobab LIMS will soon release version 1.5 with a new module for interdepartmental shipping, making it easier to transport and track samples within the Biobank or related remote sites. Currently, the development team are also working on customizations pertaining to key Client projects. Read more.
By Dominique Anderson
South African National Bioinformatics Institute, University of the Western Cape, South Africa
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Community Engagement Activities
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The eB3Kit Boosts Bioinformatics and Improves Sample Annotation at Makerere University
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B3Africa has facilitated training in use of an internet-based Bioinformatics platform (Galaxy - an open, web-based computational biomedical research server) as well as the implementation of Baobab Laboratory Information Management System (LIMS) for on-going projects at the Molecular Diagnostics laboratory at Makerere University. The eB3Kit, with its open source Baobab LIMS, as has improved sample annotation at the same laboratory. This laboratory handles student samples and projects that have limited budgets to access commercial LIMS. Two workshops have been successfully held to aimed at capacity building of the B3Africa team at Makerere University. Read More.
By Gerald Mboowa
Makerere University, Uganda
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Trainees during Bioinformatics & Next Generation Sequencing Techniques short-course at Makerere University, February 2018
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Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine (MRCG at LSHTM)
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From 25-28 September 2018, the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine (MRCG at LSHTM) hosted a B3Africa workshop in Fajara, The Gambia. The objective of the workshop was to pilot the implementation of the B3Africa informatics platform, the “eB3Kit”, at the MRCG at LSHTM. The event gathered 30 participants, including Biobank and Laboratory Managers, IT Specialists, Quality Managers from the MRCG at LSHTM, as well as B3Africa developers. Read More.
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"My dream is to have all the samples in the system with enough information that can be advertised, and then make the samples available for the scientists to use them. I think that is the ultimate goal of a biobank." Mathurin Diatta, Biobank Manager; MRCG at LSHTM
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"My dream is to improve upon what has been achieved and communicate with eB3Kit teams beyond the B3Africa project. Also, to be able to feed into the BIBBOX, Baobab LIMS and bioinformatics tools' communities of developers, so that we progressively upgrade the tools, to the benefit of our unit, and of science." Kekuta Kandeh, IT Client Support Specialist, MRCG at LSHTM
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Ethical and Legal Guidange and Tools for Sample and Data Sharing Within and Across Continents
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The B3Africa team working on ethical and legal issues (work package 1 - WP 1) elaborated a pathway to sample and data sharing across Africa and between Africa and Europe observing ethics and regulations for personal and scientific data protection (the Ethical and Legal Framework for the B3Africa Platform). A series of guides and tools have been produced:
- Model Data Management Policy;
- Checklist - For a good governance of transcontinental collaborative biobank research;
- African States-EU Member States/EU Member States-African States Data Transfer Agreement Guide;
- Informed Consent Template for Biobank and registry-based research (prospective samples);
- Material Transfer Agreement Template for material transfer between the African States-EU Member States/EU Member States-African States. Read More
By Olga Tzortzatou
Uppsala University, Sweden
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Participants to the B3Africa Ethics and Regulation Workshop, April 2016, The Gambia
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The Research Community Welcomes Galaksio, an Accessible and User-Friendly Interface to Run Galaxy Bioinformatics Workflows
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What Galaksio does is that it extracts the workflows available to a user on a Galaxy server and presents them in a user friendly manner. This enables us to maintain a very small code base while bringing the benefits of the rapid advancements of the Galaxy project to our users. This means that a laboratory can automatically upload sequencing data etc. to Galaxy and have users access it either through Galaksio to run predetermined best practice workflows or through Galaxy itself. We will also have a Galaxy tool available which retrieves the data from Baobab LIMS in JSON format and converts it into tabular data in Galaxy. Users can then select the columns of interest and merge metadata about samples with the experimental data uploaded to Galaxy for quality verification and further analysis. Read More.
By Tomas Klingström
Swedish University of Agricultural Sciences, Sweden
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Collecting data and making sure that it is an accurate representation of reality as possible is one the most difficult and underappreciated tasks of research. In the picture we are describing the use of the eB3Kit for phenomics research where we will try to make additional modules available (current BIBBOX apps in purple).
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Launch of the Biobank Learning Platform: Free Resources for Biobankers, Researchers, IT Specialists and More!
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The Biobank Learning platform has been developed to host learning and training material developed over the course of the B3Africa project. It includes more than 80 learning resources covering six main categories:
- IT infrastructure for biobanks (the eB3Kit, the BIBBOX, the BCNet Catalogue);
- Sample and data collection (mobile data collection with ODK);
- Sample and data management (Baobab LIMS, MIABIS, MTAs);
- Bioinformatics (Galaksio, Galaxy and link to other learning platforms);
- Ethical, legal and social issues;
- Quality and accountability
Read more
By Dominique Meunier
International Agency for Research on Cancer
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Create an account now and join a dynamic community of biobank and research professionals actively involved in continuous professional development!
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The B3Africa Project Recognised as a Research Success Story on the EU Portal
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Announcements and Latest Publications
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Sveriges Lantbruksuniversitet (SLU), Sweden; Biobanking and Biomolecular Resources Research Infrastructure Consortium (BBMRI-ERIC), Austria; Karolinska Institutet (KI), Sweden; Centre for Research Ethics & Bioethics (CRB) at Uppsala University, Sweden; University of the Western Cape (UWC), South Africa; Makerere University (MAK), Uganda; Stellenbosch University (SU), South Africa; International Agency for Research on Cancer (IARC), France; International Livestock Research Institute (ILRI), Kenya; Medizinische Universität Graz (MUG), Austria; and Institute of Human Virology Nigeria (IHVN), Nigeria.
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B3Africa Project Coordinator
Erik Bongcam-Rudloff (Erik.bongcam@slu.se)
BIBBOX: Open Source Software Toolbox for Biobanks
http://bibbox.bbmri-eric.eu/
Heimo Müller (heimo.mueller@medunigraz.at)
Baobab LIMS
https://baobablims.org/
Dominique Anderson (dominique@sanbi.ac.za)
Galaksio App and Galaxy in the eB3Kit
Tomas Klingström (tomas.klingstrom@slu.se)
Biobank Learning (online platform and upcoming training App)
http://biobanklearning.iarc.fr/
Dominique Meunier (meunierd@iarc.fr)
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