International Livestock Research Institute (ILRI) Training Fellowship 2021
The Biosciences eastern and central Africa – International Livestock Research Institute (BecA-ILRI) Hub (Nairobi, Kenya), in partnership with its UK-based partners the John Innes Centre (JIC), the Earlham Institute (EI) and Oxford Nanopore Technologies (ONT), launches an intensive training programme in genomics and bioinformatics, called Third-generation genomics and bioinformatics for agribiosciences in Africa.
Application Deadline: 31st October 2020 23:59 UTC.
About the Award: The partners have long-standing experience in developing capacity to apply agricultural biosciences in Africa. We are aware of the current bottlenecks in scientific research for the improvement of African agriculture, one of which is the lack of skills in biological data analysis. Therefore, in 2018, together with our partners at JIC and EI, we launched the ABCF Bioinformatics Community of Practice (BixCoP), an eight-month residential training which gave 14 early-career scientists from eight African countries the chance to gain and apply critical skills in bioinformatics data analysis, including programming (Linux and shell scripting/Python/R), NGS analyses, quantitative genetics and phylogenetics. We also ran a Train-the-Trainer module to formally prepare the trainees in how to distribute their expertise in their own communities. This training was widely praised for its quality.
The world of genomics is shaken by a revolution brought about by a new generation of portable, versatile, third-generation sequencing devices that are radically upscaling the ability for researchers to generate and analyze high-quality genomic data, inducing a paradigm shift in the way we look at full genomes and their variation. Cognisant of these advances, the BecA-ILRI Hub now proposes a new training program to equip African scientists with the skills to deploy third-generation genomics, particularly for agribiosciences. The training will largely focus on Nanopore sequencing platforms, but a general background on other sequencing platforms will be provided. The training is designed in three phases, the first two phases being residential in ILRI (Nairobi, Kenya), and a third phase being conducted remotely at the participants’ home institutions. Below is a summary of the activities envisioned as part of this programme:
- Develop phase: during four months, participants will be exposed to in-depth training modules on molecular biology and bioinformatics skills for 3rd generation sequencing (high molecular weight DNA extraction protocols, Unix command line, Python programming, 2nd and 3rd generation genomics, theory and practice of genome assembly, etc). These training modules will comprise formal lectures and a significant fraction of hands-on sessions. Besides the series of lectures delivered by internationally recognized scientists, a team of tutors (including trainees from the 2018-2020 BixCoP) will provide ad-hoc supervision to trainees during individual and group exercises.
- Demonstrate phase: intertwined with the Develop phase and extending for 1.5 month beyond it, this phase will see the trainees engage in project-based learning, building on the skills learnt during the Develop phase, and demonstrate their use in real-life research projects in genomics for agriculture or conservation co-designed with the training team.
- Deploy phase: during this last phase of the training, the trainees will return to their home institution, where they will launch a small third-generation genomics unit and implement a research project to address agricultural challenges with direct relevance to their home country or region. Wherever possible, this project will be integrated into research partnerships with ILRI or another OneCGIAR institute in the home country. Trainees will benefit from the support of highly experienced mentors from the BecA-ILRI Hub, its UK-based partners, and the One CGIAR consortium.
This training project will offer a dozen fellowships only: in line with our experience with the Bioinformatics CoP program, we will focus on the quality of the training program and the internal cohesion in the cohort of trainees, rather than on numbers. With support tailored to the trainees all through to the Deploy phase, we expect that this training will have ripple effects, with trainees returning to their home institutions to become emerging leaders in the fields of genomics and bioinformatics: “train the few to impact the many”. Therefore, applications will be rigorously screened, aiming at recruiting the best candidates in the most committed home institutions with the most promising and impactful research projects. Within this framework, reviewers will pay careful attention to achieving gender and geographic balance.
Eligibility: In order to guide potential applicants, we set out the following requirements, listed in no particular order:
- The call is open to citizens of African countries affiliated with a research institution on the continent.Applicants will have to demonstrate active support from their home institution. By “support”, we mean administrative and financial support, exempli gratia commitment to discharge the applicants from professional tasks they would have to conduct during the period of the training, financial support to help the returning trainee set up their research project in the Deploy phase, commitment to provide the trainee with a conducive environment for those research activities as well as forthcoming local training activities led by the trainee in coordination with the programme’s managing team, etc.
- The applicant’s home institution should already have a minimal molecular biology lab, with basic equipment for DNA extraction and quality checking, polymerase chain reaction (PCR) and gel electrophoresis.
- The applicant’s home institution should commit to equip itself with a MinION starter pack or any other sequencing device enabling native single-molecule sequencing, as well as commit to support the returning trainee with the other start-up costs for their Deploy project (cf. section “Costs/Funding” above).
- Applicants must have a well-thought project in mind, through which they will make use of long-reads genomics as soon as they return to their home institution (Deploy phase)
- Applicants must have earned an MSc in biological sciences, genetics, bioinformatics, biostatistics, biotechnology, agricultural sciences, or other related fields.
Eligible Countries: African countries
To be Taken at (Country): Nairobi, Kenya
Number of Awards: 12
Value of Award:
- Thanks to funding from the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) and Department for International Development (DfID, now FCDO), the Bill and Melinda Gates Foundation and Oxford Nanopore Technologies, all costs pertaining to the residential training (Develop and Demonstrate phases) will be met by the program, including return flight tickets from the country of residence, accommodation costs in Nairobi and a monthly allowance covering subsistence costs.
- Costs falling outside the residential training period (i.e. Deploy phase) will not be covered by the training program.
- It is expected that the trainees’ home institutions will demonstrate their involvement in the training program by making a formal commitment to support the returning trainee in establishing a minimal third-generation sequencing platform based on the Oxford Nanopore MinION system (or any other third-generation sequencing technology) throughout the Deploy phase. The initial setup costs of this will depend on the focus and scale of the platform, but are likely to be in the range of US$ 5,000 to 10,000, not including staff costs.
- Please note these are funds the applicant’s institution (together with its potential collaborators and partners) commits to invest in their own research platform, NOT a fee to be paid for the applicant to participate in the programme. These funds do not need to be available yet at the point of application, but a commitment letter signed by the relevant authority within the applicant’s institution must be enclosed.
- Applicants are advised to start the process of getting this commitment from their institutions early enough to get it approved in time for the application deadline.
- We encourage developing collaborations with in-country projects led by ILRI or another OneCGIAR institute, to tackle research questions with direct impact of third-generation sequencing technologies on agricultural production. Such type of work include projects on the development of genetic resources for underutilized crops and breeds, on in-field disease diagnostics, on the discovery of genomic structural variations linked with disease or productivity traits, etc.
Duration of Award: 8 months starting April 2021
How to Apply: Applications will be received online only. Applicants are asked to fill in the form at (URL) and upload the following supporting documents:
- A curriculum vitae (maximum 3 A4 pages: please be aware that we will only read the first three pages in case the uploaded file is longer).
- Transcript of the highest degree earned in any of the fields named in item (6) of the list in the previous section
- A personal cover letter (maximum 1 A4 page) addressed to Head of Capacity Development highlighting key features of the applicant that make them the right fit for this programme
- A support letter (maximum 1 A4 page) signed and stamped by a senior person from the home institution, e.g. a director, head of department or group leader able to commit research funds, indicating support as exemplified in item (2) of the list in the previous section.
In case of any questions that are not addressed by the present application guidelines, potential applicants can direct such questions to (provide an online Q/A space through which potential applicants can post questions and we reply “in the open”)