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Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

ABSTRACT: The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.

SUBMITTER: Ahmed AE

PROVIDER: S-EPMC7194140 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

Ahmed Azza E AE Mpangase Phelelani T PT Panji Sumir S Baichoo Shakuntala S Souilmi Yassine Y Fadlelmola Faisal M FM Alghali Mustafa M Aron Shaun S Bendou Hocine H De Beste Eugene E Mbiyavanga Mamana M Souiai Oussema O Yi Long L Zermeno Jennie J Armstrong Don D O'Connor Brian D BD Mainzer Liudmila Sergeevna LS Crusoe Michael R MR Meintjes Ayton A Van Heusden Peter P Botha Gerrit G Joubert Fourie F Jongeneel C Victor CV Hazelhurst Scott S Mulder Nicola N

AAS open research 20180101

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Bu ...[more]

PMID: 32382696

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Project description:BackgroundA steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure.ResultsCloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds.ConclusionsCloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Dataset Information

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

Publications

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

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