Browsing by Author "Panji, Sumir"

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    Open Access
    African Genomic Medicine Portal: A Web Portal for Biomedical Applications
    (2022-02-11) Othman, Houcemeddine; Zass, Lyndon; da Rocha, Jorge E B; Radouani, Fouzia; Samtal, Chaimae; Benamri, Ichrak; Kumuthini, Judit; Fakim, Yasmina J; Hamdi, Yosr; Mezzi, Nessrine; Boujemaa, Maroua; Okeke, Chiamaka Jessica; Tendwa, Maureen B; Sanak, Kholoud; Chaouch, Melek; Panji, Sumir; Kefi, Rym; Sallam, Reem M; Ghoorah, Anisah W; Romdhane, Lilia; Kiran, Anmol; Meintjes, Ayton P; Maturure, Perceval; Jmel, Haifa; Ksouri, Ayoub; Azzouzi, Maryame; Farahat, Mohammed A; Ahmed, Samah; Sibira, Rania; Turkson, Michael E E; Ssekagiri, Alfred; Parker, Ziyaad; Fadlelmola, Faisal M; Ghedira, Kais; Mulder, Nicola; Kamal Kassim, Samar
    Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available.
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    Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
    (BioMed Central, 2018-11-29) Baichoo, Shakuntala; Souilmi, Yassine; Panji, Sumir; Botha, Gerrit; Meintjes, Ayton; Hazelhurst, Scott; Bendou, Hocine; Beste, Eugene d; Mpangase, Phelelani T; Souiai, Oussema; Alghali, Mustafa; Yi, Long; O’Connor, Brian D; Crusoe, Michael; Armstrong, Don; Aron, Shaun; Joubert, Fourie; Ahmed, Azza E; Mbiyavanga, Mamana; Heusden, Peter v; Magosi, Lerato E; Zermeno, Jennie; Mainzer, Liudmila S; Fadlelmola, Faisal M; Jongeneel, C. V; Mulder, Nicola
    Abstract Background The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and secondary input data through several computationally-intensive processing steps using different software packages, where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and easy-to-use workflows is particularly challenging. Results H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for use by members of the H3Africa consortium and the international research community. Conclusion The H3ABioNet workflows have been implemented in view of offering ease of use for the end user and high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network.
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    The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research
    (2019-12-30) Kumuthini, Judit; Zass, Lyndon; Panji, Sumir; Salifu, Samson P; Kayondo, Jonathan K; Nembaware, Victoria; Mbiyavanga, Mamana; Olabode, Ajayi; Kishk, Ali; Wells, Gordon; Mulder, Nicola J
    Abstract Background Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)‘s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation. Results The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD. Conclusion To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.