BOSS-miniprojects

The third phase, Hack, of the BOSS Events consists of the miniprojects. Our participants get to learn about reproducibility by reproducing research that has been done before or contributing to ongoing work. The projects will allow our participants to practice the skills they have learnt througout the workshops.

The Projects

Open Science in Africa.

Aim:

The study will aim at trying to describe the current status of Open Science in Africa. This will involve coming up with a review through literature search from the current published manuscript on Open Science in Africa. Open Science in Kenya: Where are we? Manuscript will serve as a starting point. The aim is to expand the study started in 2018.

Manuscript:

Mwangi, K. W., Mainye, N., Ouso, D. O., Esoh, K., Muraya, A. W., Mwangi, C. K., Naitore, C., Karega, P., Kibet-Rono, G., Musundi, S., Mutisya, J., Mwangi, E., Mgawe, C., Miruka, S., Kibet, C. K., & OpenScienceKE Collaborators (2021). Open Science in Kenya: Where Are We?. Frontiers in research metrics and analytics, 6, 669675. https://doi.org/10.3389/frma.2021.669675

Objective:

• Come up with a detailed report answering the following:
• How are other continents spearheading Open Science in comparison to Africa
• What are some of the successes in Open Science Initiative in Africa
• What challenges are experienced in spearheading Open Science in Africa
• What recommendation can be suggested
• How COVID has affected research in Kenya

Comment on this issue to take part in this project.

Open Science Research Data Management Handbook.

Aim:

Create a handbook to facilitate proper research data management in Resource constrained settings. In this project, the participants will be expected to evaluate and compare the various genomics data management approaches that are available and to test how easy it is to set-up and use the tools. The focus is on genomics.

Guide: Use the TuringWay Handbook as a guide on how to create the book. In the Turing-way: Welcome — The Turing Way

Objective: Answer the following questions:

• What platforms are available for use in resource constrained settings, especially free or cheap ones
• How easy are they to set-up? Here, we are interested in tools that can easily be set up in a lab without very experience system administrators
• Explore the role of research data management policies in guiding the implementation of these tools.

Comment on this issue to take part in this project

Metagenomics Analysis

Aim:

The study will aim at reproducing a meta-genomics study performed in Kenya. The study and data will be selected and obtained from the GOLD or any database. Participants will be required to understand the study, reproduce it using the same or alternative bioinformatics tools used in the study and report on information obtained from analysis.

Manuscript:

Langat, S. K., Eyase, F., Bulimo, W., Lutomiah, J., Oyola, S. O., Imbuga, M., & Sang, R. (2021). Profiling of RNA Viruses in Biting Midges (Ceratopogonidae) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis. mSphere, 6(5), e0055121. https://doi.org/10.1128/mSphere.00551-21

Objective:

• Come with a detailed report answering the following:
• Describe the metadata and data made available in the database and their formats
• The tool used and an alternative that can be used in the pipeline
• Conclusions obtained from analysis using the pipeline, or address a gap/recommendation mentioned in the same study

Comment on this issue to take part in this project

Plant Genome Assembly

Aim:

The study uses several genomic and bioinformatics approaches. In this project, participants will be required to reproduce the genomic analysis carried out in the study. The data will be available from NCBI. You are expected to: Download the sequence data programmatically, carry out DNA sequence pre-processing and de novo assembly and perform genome annotation of the plant of interest.

Manuscript:

Chang, Y., Liu, H., Liu, M., Liao, X., Sahu, S. K., Fu, Y., Song, B., Cheng, S., Kariba, R., Muthemba, S., Hendre, P. S., Mayes, S., Ho, W. K., Yssel, A. E. J., Kendabie, P., Wang, S., Li, L., Muchugi, A., Jamnadass, R., … Liu, X. (2018). The draft genomes of five agriculturally important African orphan crops. 8, 1–16. https://doi.org/10.1093/gigascience/giy152

Objectives: Come with a detailed report answering the following:

• Are you able to determine genome location associated with crucial agronomic traits?
• Are you able to arrive at similar conclusions as those in the paper? Why or why not?
• Are the descriptions in the methodology section detailed for reproducibility? If not, what could you have done to improve reproducibility?

Comment on the issue to take part in this project.

Viral Miniproject

Aim:

The study will use bioinformatics approaches. In this project, participants will be required to use the provided files described in the manuscript to perform data preprocessing, variant calling, alignment, assembly and phylogenetic analysis as described by the manuscript. Participants will use any pipeline used in the study, interpret the output files, critique it, compare with other available pipelines or even come up with a better pipeline.

Manuscript:

Casimiro-Soriguer, C. S., Perez-Florido, J., Fernandez-Rueda, J. L., Pedrosa-Corral, I., Guillot-Sulay, V., Lorusso, N., Martinez-Gonzalez, L. J., Navarro-Marí, J. M., Dopazo, J., & Sanbonmatsu-Gámez, S. (2021). Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain). Viruses, 13(5), 836. https://doi.org/10.3390/v13050836

Objective:

• Come with a detailed report answering the following:
• Describe all components of the pipeline used in the manuscript.
• Was it easy to utilize the pipeline? If not why?
• How can you compare it with other pipelines such as Galaxy?

Comment on the issue to take part in this project

Project Leads

The project leads of each project are partners of BHKi and OpenScienceKe.

Participants

Our workshop participants will proceed to this phase and will be divided into groups to take part in different projects.

Results and conclusions

All the projects will adopt an open approach and will be published or updated in GitHub. The participants will also present their works in the BOSS conference happening in March 2022.

How to contribute

Follow the individual project GitHub repos to contribute.

Code of Conduct

All rules and regulations stipulated in CoC of both BHKi and Open Science Kenya still apply. However, below are some specific rules and regulations that will apply as you work in teams in your mini project/hackathon:

• Teamwork is highly encouraged. This means that all participants in your team should be allowed to contribute his/her ideas.
• All participants should be accommodated keeping in mind that there are slow and fast learners.
• Every mini project will have its HPC account, this means that duplicate work is highly discouraged. A team lead should be selected to spearhead activities of the account.
• All interested participants should be given a chance to submit jobs. However, commitment and hard work will be called upon by every participant.
• All mini projects have mentors, they will offer support and advice throughout your period of working on your mini project. However, the only means of communication will be through slack and/or email. Specific day(s) of the week and time will be communicated to you prior to your commencement.
• Reports and presentations at the end of the mini projects will be expected and used to evaluate your success.
• Not all will be straightforward therefore thorough reading is encouraged
DISCLAIMER: Creativity is a valueless trait for every bioinformatician.