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Sustainable collaborative research between SLU, Uppsala and ILRI in the field of genomics, bioinformatics and immunoinformatics
In January 2008 connectivity between the Research and Education Communities in Europe and Sub-Saharan Africa was established with a 1 Gbps between the UbuntuNet Alliance and GÉANT.
Dr. Erik Bongcam-Rudloff, Department of Animal Breeding and Genetics, (HGEN) - Sweden Dr. Etienne de Villiers, ILRI/BeCa, Nairobi, Kenya
Main/Partner organisations
Swedish University of Agriculture (SLU) International Livestock Research Institute/ Biosciences eastern and central Africa (BecA) Hub.
Contact Details
Dr. Erik Bongcam-Rudloff, Erik.Bongcam [AT] hgen.slu.se
Department of Animal Breeding and Genetics, (HGEN)
Box 7023, 750 07
Uppsala, Sweden
Dr. Etienne de Villiers, Email: e.villiers [AT] cgiar.org, ILRI/BeCa, Nairobi, Kenya
Objectives and short summary of activities
The need for enhanced bioinformatics capacity as a core competency in biosciences is rapidly increasing as large volumes of data on genomes become available, and with this the demand to mine such data in support of research. Stakeholders of the Biosciences eastern and central Africa ( BecA) have identified capacity building in this area as among the highest priorities to support biosciences application in agriculture. Bioinformatics is an integral part of much of research in modern biology, medicine, veterinary and agricultural sciences. Basic requisites for bioinformatics applications are databases, analysis tools and expert knowledge. The most well known databases are those containing information on the genomes of different species, including the bovine, horse and chicken and several crop genomes such as rice. A key need in this new and rapidly developing field is adequate number of skilled human people. In order to provide access to current knowledge and information technology tools to support bioinformatics, genomics and immunoinformatics, this project developed collaboration with other CGIAR institutes, regional Institutes and Universities and International entities such as SLU and Linnaeus Centre for Bioinformatics.
Research activities carried and out and scientific data generated
The project created the eBioKit an autonomous server containing all public genomic databases and installed the eBioKits on 12 countries in Africa. The eBioKits were used to analyse data produced by Next Generation Sequencing platforms as well as many different project ranging from Bacterial to Mammalian Genomes. Work is under progress and reports will be generated at the end of 2010 and beginning of 2011. This project will also benefit from the newly started “Next Generation Sequencing Data Analysis Network” (www.nextgenerationsequencing.org).
Principal outcomes and documentation (plus link to case studies)
The data generated by these studies includes • Whole genome sequence data • Biological Databases • Bioinformatics tools • Course materials
More than 150 students participated on the courses organized by the SLU/ILRIBeCa team. Two more workshops were organized in Mauritius and Zimbabwe. Several new courses are now financed by different organizations and will take place in 2011, two by WHO, one by EMBO and one by ABioNET/EMBnet.
Several publications will soon be submitted, some reports were published on EMBnet.Journal (http://journal.embnet.org/index.php/embnetjournal)
Other potential application areas/ actual spillovers
The eBioKits are also in use by the SanBio network (Southern Africa Network for Biosciences, http://www.nepadst.org/sanbio/ ) and will be used as the basis for a data analysis kit to be developed by the COST Action SeqAhead to start in 2011. The BeCa hubs include the following countries: Burundi, Cameroon, Central Africa Republic, Congo Brazzaville, Democratic Republic of Congo, Equatorial Guinea, Eritrea, Ethiopia, Gabon, Kenya, Madagascar, Rwanda, Sao Tome and Principe, Somalia, Sudan, Tanzania, Uganda. The potential to deploy eBioKits and develop the same curriculum for all hubs is being investigated. The same idea and project is under way under the umbrella of the SanBio bioinformatics area.
Funding source
Public Co-funding
Project start date
Funding duration
Status
on-going
Resources employed
All resources are incorporated on the eBIoKit, those include ENSEML (animals, plants, protozoan, bacteria), the EMBOSS package with a web-based front end. wEMBOSS, Galaxy, MRS, BioMart and many more. Tutorials are embedded via a wiki interface.
Cost-Benefit analysis of access to e-infrastructure resources:
Running / Recurring cost reduction and elimination of costs of data media (Disks) More funding to research grants
Facilitates mentoring and e-conferencing Operational efficiency
Strengthen position of local scientists with cutting edge science without depending on unreliable Internet connections. Capacity building in the area of bioinformatics.
Time saving Enhance speedy and quality research
Courses organized in situ and via video/voice conferencing over IP (Marratech and Skype)
Accessibility
Reduction of potential risks of unauthorised access to confidential data, all data analysis can take place without being connected to the Internet.
Environmental impact
Reduced travel needs
e-Infrastructure potential All eBioKits are independent of Internet but a problem to be solved is the update of the databases. This database update is an imperative need that should be solved with new approaches.
